Physiology or Medicine
Victor Ambros and Gary Ruvkun discovered microRNA, a new class of tiny RNA molecules that play a crucial role in gene regulation. Their groundbreaking discovery in the small worm C. elegans revealed a completely new principle of gene regulation. This turned out to be essential for multicellular organisms, including humans. MicroRNAs are proving to be fundamentally important for how organisms develop and function.
Physics
John Hopfield introduced a spin model that can store and reconstruct information. Geoffrey Hinton built on Hopfield’s idea to invent the Boltzmann Machine, that is able to learn from examples to reconstruct a set of desired patterns. He also popularized and improved Backpropagation of Errors, a method actually used in today’s advanced AI technology (e.g. Deep Learning).
Chemistry
The Nobel Prize in Chemistry 2024 is about proteins, life’s ingenious chemical tools. David Baker has succeeded with the almost impossible feat of building entirely new kinds of proteins. Demis Hassabis and John Jumper have developed an AI model to solve a 50-year-old problem: predicting proteins’ complex structures. These discoveries hold enormous potential.
Seminars
Date:
17
November, 2024
Sunday
Hour: 13:15-14:30
The Clore Center for Biological Physics
Yet Another Approach to Loschmidt's Paradox
Dr. Lev Melnikovsky | Department of Molecular Chemistry and Materials Science
Protein function is the combined product of chemical and mechanical interactions encoded in the gene. Thus, the function of enzymes relies on finetuning the chemical groups at the active site, but also on large-scale mechanical motions, allowing enzymes to bind to substrates selectively, reach the transition state, and release products. We will discuss recent work aiming to probe directly the linkage between these collective internal motions and the functionality of enzymes, using nano-rheological measurements, AI-prediction of point mutation effects, and physical theory. This work proposes a physical view of enzymes as viscoelastic catalytic machines with sequence-encoded mechanical specifications, which are modulated via long-ranged force transduction.
In this two-part talk, I will try to cover two separate lines of research: Machine learning of antibiotic resistance and AI-driven Science. In the first half, I will describe our efforts to understand and predict antibiotic resistance at the single patient level. I will describe a series of experimental-computational methodologies for following and identifying recurrent patterns in the evolution of antibiotic resistance in the lab and in the clinic. Combined with machine-learning approaches applied to electronic patient records, these tools lead to predictive diagnostics of antibiotic resistance and algorithms for personalized treatments of microbial infections. In the second part of the talk, we will shift gear and talk about AI-driven science. I will describe and demo “data-to-paper”: a platform that autonomously guides LLMs (like ChatGPT) to perform entire research cycles. Provided with data alone, data-to-paper can raise hypotheses, design research plans, write and debug analysis codes, generate and interpret results, and write complete research papers. Automatic information-tracing through the process creates manuscripts in which results, methods and data are programmatically chained. Our work thereby demonstrates a potential for AI-driven acceleration of scientific discovery while enhancing, rather than jeopardizing, traceability, transparency and verifiability. I will describe the strengths of the approach as well as limitations and challenges.
Prof. Kishony would be available to discuss with students and
postdocs after his seminar (2:15 pm - 3 pm).
So we encourage interested students and postdocs to stay after his talk!
FOR THE LATEST UPDATES AND CONTENT ON SOFT MATTER AND BIOLOGICAL PHYSICS AT THE WEIZMANN, VISIT OUR WEBSITE: https://www.biosoftweizmann.com/
Seminars
Date:
13
October, 2024
Sunday
Hour: 13:15-14:30
The Clore Center for Biological Physics
Statistical Physics of Multicomponent Systems with Non-Reciprocal Interactions
After a brief introduction related to ultralight (pseudo) scalar dark matter, we shall describe the current status of searches for ultralight dark matter (UDM). We explain why modern clocks can be used to search for both scalar and axion dark matter fields. We review existing and new types of well-motivated models of UDM and argue that they all share one key ingredient - their dominant coupling is to the QCD/nuclear sector.
This is very exciting as we are amidst a revolution in the field of dark matter searches as laser excitation of Th-229 with effective precision of 1:10^13 has been recently achieved, which as we show, is already probing uncharted territory of models. Furthermore, Th-229-based nuclear clock can potentially improve the sensitivity to physics of dark matter and beyond by factor of 10^10! It has several important implications to be discussed.
Seminars
Date:
07
July, 2024
Sunday
Hour: 13:15-14:30
The Clore Center for Biological Physics
What does the system “care about”?
Empirical approaches to identifying biological regulation
Prof. Naama Brenner | Dept. of Chemical Engineering & Network Biology Research Lab, Technion
Biological systems regulate their action at multiple levels of organization, from molecular circuits to physiological function. This “homeostasis” maintains stability of the system in the face of external and internal perturbation. How exactly this is achieved remains a topic of ongoing investigation; challenges are high dimensionality, many coupled positive and negative feedback loops, conflicting regulation demands and interaction with the environment.
Here I will introduce an empirical approach to the fundamental question – how do we know what it is that the system really “cares about”? What variable, or combination of variables, is under regulation? Two data-driven methods will be presented. one based on statistical analysis and applied to bacterial growth and division, revealing a hierarchy of regulation – from tightly regulated to sloppy variables. The second is based on a machine-learning algorithm we developed to identify regulation with minimal assumptions. This provides a different angle on the problem and highlights directions for future research.
FOR THE LATEST UPDATES AND CONTENT ON SOFT MATTER AND BIOLOGICAL PHYSICS AT THE WEIZMANN, VISIT OUR WEBSITE: https://www.biosoftweizmann.com/
Seminars
Date:
23
June, 2024
Sunday
Hour: 12:45-14:30
The Clore Center for Biological Physics
The role of sign indefinite invariants in shaping turbulent cascades.
Our work answers a nearly 60-year quest to derive the turbulent spectrum of weakly interacting internal gravity waves from first principles. The classical wave-turbulence approach didn’t work, as the underlying equation, both in 2D and 3D, is an anisotropic, non-canonical Hamiltonian equation.
A key consequence of the non-canonical Hamiltonian is the conservation of a sign-indefinite quadratic invariant alongside the sign-definite quadratic energy. In 2D, this allows us to derive a much simpler kinetic equation. We leverage this simplification into the derivation of solutions of the kinetic equation, one of which is the turbulent spectrum of weakly interacting 2D internal gravity waves. Our spectrum exactly matches the phenomenological oceanic Garrett-Munk spectrum in the limit of large vertical wave numbers and zero rotation.
This talk is based on recent joint works with Oliver Bühler and Jalal Shatah
arXiv:2311.04183 (to appear soon in PRL).
arXiv:2406.06010.
FOR THE LATEST UPDATES AND CONTENT ON SOFT MATTER AND BIOLOGICAL PHYSICS AT THE WEIZMANN, VISIT OUR WEBSITE: https://www.biosoftweizmann.com/
Colloquia
Date:
20
June, 2024
Thursday
Hour: 11:15-12:30
Physics colloquium
Stochastic resonance in polymer solution channel flow
Prof. Victor Steinberg | Weizmann Institute of Science
A cooperative resonance effect in a stochastic nonlinear dynamical system subjected to external weak periodic forcing, called stochastic resonance (SR), has been extensively studied for the past forty years. Here I discuss the experimentally unexpected observation of SR above an elastic non-modal instability of an inertia-less channel flow of polymer solution (much more complicated than stochastic dynamical flow) due to finite-size white noise perturbations. This flow is shown to be linearly stable similar to Newtonian parallel shear flow. First, I briefly describe viscoelastic flow with curved streamlines, where linear elastic normal mode instability at the critical Weissenberg number, Wic, has been observed and characterized, and the elastic instability mechanism has been explained and experimentally validated. Furthermore, at Wi>>Wic, “elastic turbulence” (ET), a chaotic flow arising via secondary instability, is experimentally discovered, characterized and theoretically explained, while elastic instability in straight channel flow is found from the direct transition from laminar to chaotic flow in the transition flow regime is found. At the secondary instability, ET is observed, and further on the next transition to the unexpected drag reduction flow regime takes place, accompanied by elastic waves previously discovered and characterized earlier. Moreover, we propose and experimentally validate a mechanism of amplification of the wall normal fluctuating vortices by the elastic waves. The elastic waves play the key role in the energy transfer from the main flow to the wall-normal fluctuating vortices. Finally, we report on recently discovered SRs only in a limited subrange of weak elastic waves just above Wic, their characterization, and their role in the transition to a chaotic flow.
Seminars
Date:
10
June, 2024
Monday
Hour: 13:00-14:00
The Clore Center for Biological Physics- Special seminar
Mixing Artificial and Natural Intelligence: From Statistical Mechanics to AI and Back
Dr. Michael (Misha) Chertkov | University of Arizona
This presentation will outline recent evolution of AI methodologies, focusing on the emergence of Diffusion Models of AI inspired by non-equilibrium statistical mechanics, Transformers, and Reinforcement Learning. These innovations are revolutionizing our approach to reduced, Lagrangian turbulence modeling and are instrumental in formulating and solving new challenges, such as swimming navigation in chaotic environments.
More generally, attendees will gain insights into the synergy between AI and natural sciences and understand how this symbiosis is shaping the future of scientific research. This comprehensive vision is relevant to theoretical physicists, applied mathematicians, and computer scientists alike.
Colloquia
Date:
10
June, 2024
Monday
Hour: 11:15-12:30
Physics Colloquium
OBSERVATION OF FRACTIONAL QUANTUM ANOMALOUS HALL EFFECT
Prof. Xiaodong Xu | University of Washington, Seattle, WA
The interplay between spontaneous symmetry breaking and topology can result in exotic quantum states of matter. A celebrated example is the quantum anomalous Hall (QAH) effect, which exhibits an integer quantum Hall effect at zero magnetic field due to topologically nontrivial bands and intrinsic magnetism. In the presence of strong electron-electron interactions, fractional-QAH (FQAH) effect at zero magnetic field can emerge, which is a lattice analog of fractional quantum Hall effect without Landau level formation. In this talk, I will present experimental observation of FQAH effect in twisted MoTe2 bilayer, using combined magneto-optical and -transport measurements. In addition, we find an anomalous Hall state near the filling factor -1/2, whose behavior resembles that of the composite Fermi liquid phase in the half-filled lowest Landau level of a two-dimensional electron gas at high magnetic field. Direct observation of the FQAH and associated effects paves the way for researching charge fractionalization and anyonic statistics at zero magnetic field.
Reference
1. Observation of Fractionally Quantized Anomalous Hall Effect, Heonjoon Park et al., Nature, https://www.nature.com/articles/s41586-023-06536-0 (2023);
2. Signatures of Fractional Quantum Anomalous Hall States in Twisted MoTe2 Bilayer, Jiaqi Cai et al., Nature, https://www.nature.com/articles/s41586-023-06289-w (2023);
3. Programming Correlated Magnetic States via Gate Controlled Moiré Geometry, Eric Anderson et al., Science, https://www.science.org/doi/full/10.1126/science.adg4268 (2023).
Colloquia
Date:
06
June, 2024
Thursday
Hour: 11:15-12:30
Physics Colloquium
Emergent Quantum Phenomena in Crystalline Multilayer Graphene
Condensed matter physics has witnessed emergent quantum phenomena driven by electron correlation and topology. Such phenomena have been mostly observed in conventional crystalline materials where flat electronic bands are available. In recent years, moiré superlattices built upon two-dimensional (2D) materials emerged as a new platform to engineer and study electron correlation and topology. In this talk, I will introduce a family of synthetic quantum materials, based on crystalline multilayer graphene, as a new platform to engineer and study emergent phenomena driven by many-body interactions. This system hosts flat-bands in highly ordered conventional crystalline materials and dresses them with proximity effects enabled by rich structures in 2D van der Waals heterostructures. As a result, a rich spectrum of emergent phenomena including correlated insulators, spin/valley-polarized metals, integer and fractional quantum anomalous Hall effects, as well as superconductivities have been observed in our experiments. I will also discuss the implications of these observations for topological quantum computation.
References:
[1] Han, T., Lu, Z., Scuri, G. et al. Nat. Nanotechnol. 19, 181–187 (2024). [2] Han, T., Lu, Z., Scuri, G. et al. Nature 623, 41–47 (2023). [3] Han, T., Lu, Z., Yao, Y. et al. Science 384,647-651(2024). [4] Lu, Z., Han, T., Yao, Y. et al. Nature 626, 759–764 (2024). [5] Yang, J., Chen, G., Han, T. et al. Science, 375(6586), pp.1295-1299. (2022)
Seminars
Date:
04
June, 2024
Tuesday
Hour: 13:15-14:30
The Clore Center for Biological Physics
Flexoelectricity versus Electrostatics in Polar Nematic Liquid Crystals
In the most common phase of liquid crystals, called the nematic phase, molecules are aligned up or down along some axis, so that the net electrostatic polarization is zero. Recent experiments have found a new class of liquid crystals, called ferroelectric nematic, in which molecules align predominantly in one direction along the axis, leading to a nonzero polarization. From the perspective of statistical mechanics, the ferroelectric nematic phase has two special features. First, it has flexoelectricity, meaning that the polarization induces a splay of the molecular orientation. Second, the energy includes an electrostatic interaction, which favors a domain structure. In this talk, we discuss the competition between those two effects to control the phase behavior.
FOR THE LATEST UPDATES AND CONTENT ON SOFT MATTER AND BIOLOGICAL PHYSICS AT THE WEIZMANN, VISIT OUR WEBSITE: https://www.biosoftweizmann.com/
Seminars
Date:
26
May, 2024
Sunday
Hour: 13:15-14:30
The Clore Center for Biological Physics
Phages vs bacteria warfare: co-evolution and intelligence gathering
The warfare between bacteria and phages - viruses that infect bacteria - has been raging for billions of years. During this time both sides have evolved various attack and defense systems. In this talk I will describe 3 related projects: 1. Is there an optimal number of such defense or anti-defense systems? 2. How can different phages which prey on the same bacteria co-exist, in contradiction with the expected competitive exclusion? 3. Some phages have developed the ability to garner environmental information, enabling them to make more "intelligent" decisions. How much is such intelligence worth, in terms of other resources?
FOR THE LATEST UPDATES AND CONTENT ON SOFT MATTER AND BIOLOGICAL PHYSICS AT THE WEIZMANN, VISIT OUR WEBSITE: https://www.biosoftweizmann.com/
Colloquia
Date:
23
May, 2024
Thursday
Hour: 11:15-12:30
Physics Colloquium
Quantum Dot Physics Using Atomic Defects in Ultrathin Tunnel Barriers
Quantum dots (QDs) are conducting regions which can localize few charge carriers, and where the energy spectrum is dominated by Coulomb repulsion. QDs can be as large as few hundreds of nanometers, or as small as a single molecule, their sizes depending on their physical realization – whether in two-dimensional materials, nanowires, molecular systems.
In my talk I will describe our work on a new type of an atomically-sized QD, realized in defects residing in ultrathin two-dimensional insulators. These defect-dots are found in layered materials such as hexagonal Boron Nitride (hBN), which we study by their assembly into stacked devices. By using graphene electrodes, we are able to electronically couple to the QD, while allowing the QD energy to be externally tuned exploiting the penetration of electric field through graphene.
A consequence of the structure of our devices is that the defect QDs are placed at atomic distance to the conductors on both sides. I will show how the presence of such energy-tunable, atomically sized QDs at nanometer proximity to other conducting systems opens new opportunities for sensitive measurements, including use of QDs as highly sensitive spectrometers [1], or as single electron transistors, unique in their sensitivity to local electric fields at the nanometer scale [2]. I will discuss our future prospects of using defect QDs as quantum sensors.
References
1. Devidas, T.R., I. Keren, and H. Steinberg, Spectroscopy of NbSe2 Using Energy-Tunable Defect-Embedded Quantum Dots. Nano Letters, 2021. 21(16): p. 6931-6937.
2. Keren, I., et al., Quantum-dot assisted spectroscopy of degeneracy-lifted Landau levels in graphene. Nature Communications, 2020. 11(1): p. 3408.
We study the assembly of programmable quasi-2D DNA compartments as
“artificial cells” from the individual cellular level to multicellular communication.
We will describe work on autonomous synthesis and assembly of cellular
machines, collective modes of synchrony in a 2D lattice of ~1000
compartments, and a first look at the birth of proteins on a single DNA.
Colloquia
Date:
09
May, 2024
Thursday
Hour: 11:15-12:30
Physics colloquium
Synergistic progress in plasmas:
from fusion to astrophysics
Prof. Julien Fuchs | Laboratoire pour l’Utilisation des Lasers Intenses,
CNRS, Ecole polytechnique, France
Over the last decade, several exciting directions have been initiated by laser-driven plasmas,
e.g., compact particle accelerators, inertial fusion and laboratory astrophysics. The first has
known rapid progress, in terms of current, energy, stability; fusion has gone through a historic
step, with the news of ignition being achieved at NIF in 2022; and laboratory astrophysics has
known also spectacular developments, demonstrating the possibility to perform fully scalable
experiments relevant to various objects such as forming stars and supernovae. A particularly
interesting aspect is that all these fields are strongly synergistic, i.e., that advances in one can
push the others as well. I will present examples of such synergies, through recent results
we have obtained in all these domains, and in particular how ultra-bright neutron beams
can be developed using latest generation multi-PW lasers [1,2]. These could open interesting
perspectives in terms of cargo inspection, but also for fusion plasma measurements.
I will also show how fusion can benefit from external magnetization [3]. Finally, I will discuss
advances in laboratory astrophysics, particularly the first-stage acceleration of ions leading to
cosmic rays [4,5], understanding the universal nature of collimated outflows in the Universe [6],
and probing the intricacy of 3D magnetic reconnection [7]
[1] High-flux neutron generation by laser-accelerated ions from single-and double-layer targets, V Horný et al.,
Scientific Reports 12 (1), 19767, 2022
[2] Numerical investigation of spallation neutrons generated from petawatt-scale laser-driven proton beams,
B Martinez et al., Matter and Radiation at Extremes 7 (2), 024401, 2022
[3] Dynamics of nanosecond laser pulse propagation and of associated instabilities in a magnetized underdense
plasma, W. Yao et al., https://doi.org/10.48550/arXiv.2211.06036
[4] Laboratory evidence for proton energization by collisionless shock surfing, W Yao et al.,
Nature Physics 17 (10), 1177-1182, 2021
[5] Enhancement of the Nonresonant Streaming Instability by Particle Collisions, A Marret et al.,
Physical Review Letters 128 (11), 115101, 2022
[6] Laboratory disruption of scaled astrophysical outflows by a misaligned magnetic field, G Revet et al.,
Nature communications 12 (1), 762, 2021
[7] Laboratory evidence of magnetic reconnection hampered in obliquely interacting flux tubes, S Bolaños et al.,
Nature Communications 13 (1), 6426, 2022
We study the assembly of programmable quasi-2D DNA compartments as “artificial cells”, from the individual cellular level to multicellular communication. We will describe work on autonomous synthesis and assembly of cellular machines, collective modes of synchrony in a 2D lattice of ~1000 compartments, and a first look at the birth of proteins on a single DNA.
Seminars
Date:
07
April, 2024
Sunday
Hour: 13:15-14:30
The Clore Center for Biological Physics
Odd Mechanical Screening: From Metamaterial to Continuum Mechanics of Disordered Solids
Prof. Michael Moshe | Hebrew University in Jerusalem
Holes in elastic metamaterials, defects in 2D curved crystals, localized plastic deformations in amorphous solids and T1 transitions in epithelial tissue, are typical realizations of stress-relaxation mechanisms in different solid-like structures, interpreted as mechanical screening.
In this talk I will present a mechanical screening theory that generalizes classical theories of solids, and introduces new moduli that are missing from the classical theories. Contrary to its electrostatic analog, the screening theory in solids is richer even in the linear case, with multiple screening regimes, predicting qualitatively new mechanical responses.
The theory is tested in different physical systems, including disordered granular solids that do not have a continuous mechanical description. These materials are shown to violate energy conservation and are best described by Odd-Screening: a screening model that does not derive from an energy function. Experiments reveal a mechanical response that is strictly different from classical solid theory and is completely consistent with our mechanical-screening theory. Finally, I will discuss the relevance of this theory to 3D solids and a new Hexatic-like state in 3D matter.
Draw an arbitrary open curve on the plane and copy it multiple times to form a translationally invariant infinite trajectory. Then, incline the plane slightly and ask yourself: can one chisel a stone that will roll exactly down this infinite trajectory?
We will examine this question in practice and theory. Intriguing links to optics and quantum systems will be discussed. Bringing a tennis ball or a baseball is always recommended.
Eckmann et al. Tumbling downhill along a given curve. Am Math Soc Notices - in press.
Sobolev et al. Solid-body trajectoids shaped to roll along desired pathways. Nature 2023.
Colloquia
Date:
21
March, 2024
Thursday
Hour: 11:15-12:30
Physics Colloquium
Fractional statistics of anyons in mesoscopic colliders
In three-dimensional space, elementary particles are divided between fermions and bosons according to the properties of symmetry of the wave function describing the state of the system when two particles are exchanged. When exchanging two fermions, the wave function acquires a phase, φ=π. On the other hand, in the case of bosons, this phase is zero, φ=0. This difference leads to deeply distinct collective behaviors between fermions, which tend to exclude themselves, and bosons which tend to bunch together. The situation is different in two-dimensional systems which can host exotic quasiparticles, called anyons, which obey intermediate quantum statistics characterized by a phase φ varying between 0 and π [1,2].
For example in the fractional quantum Hall regime, obtained by applying a strong magnetic field perpendicular to a two-dimensional electron gas, elementary excitations carry a fractional charge [3,4] and have been predicted to obey fractional statistics [1,2] with an exchange phase φ=π/m (where m is an odd integer). Using metallic gates deposited on top of the electron gas, beam-splitters of anyon beams can be implemented. I will present how the fractional statistics of anyons can be revealed in collider geometries, where anyon sources are placed at the input of a beam-splitter [5,6]. The partitioning of anyon beams is characterized by the formation of packets of anyons at the splitter output. This results in the observation of strong negative correlations of the electrical current, which value is governed by the anyon fractional exchange phase φ [5,7].
[1] B. I. Halperin, Phys. Rev. Lett. 52, 1583–1586 (1984).
[2] D. Arovas, J. R. Schrieffer, F. Wilczek, Phys. Rev. Lett. 53, 722–723 (1984).
[3] R. de Picciotto et al., Nature 389, 162–164 (1997).
[4] L. Saminadayar, D. C. Glattli, Y. Jin, B. Etienne, Phys. Rev. Lett. 79, 2526–2529 (1997)
[5] B. Rosenow, I. P. Levkivskyi, B. I. Halperin, Phys. Rev. Lett. 116, 156802 (2016).
[6] H. Bartolomei et al. Science 368, 173-177 (2020).
[7] Lee, JY.M., Sim, HS, Nature Communications 13, 6660 (2022).
The communication of plants with their environment is crucial for their survival. Plants are known to use light, odors, and touch to communicate with other organisms, including plants and animals. Yet, acoustic communication is almost unexplored in plants, despite its potential adaptive value. This is the topic of the current talk. We have started exploring plant bioacoustics - what plants hear, and what they “say”. I will describe two major projects: in the first we study plant hearing, testing the responses of flowers to sounds of pollinators; in the second we investigate plant sound emission - we have shown that different species of plants emit brief ultrasonic signals, especially under stress. Using AI we can interpret these sounds and identify plant species and stress condition from the sounds. Potential implications of these projects for plant ecology, evolution and agriculture will be discussed.
The microscopic theory of superconductivity was developed by John Bardeen, Leon N Cooper and J. Robert Schrieffer. It is among the most beautiful and outstanding achievements of modern scientific research. Almost half a century passed between the initial discovery of superconductivity by Kamerlingh Onnes and the theoretical explanation of the phenomenon. During the intervening years the brightest minds in theoretical physics tried and failed to develop a microscopic understanding of the effect. I will discuss some of those unsuccessful attempts to understand superconductivity. This not only demonstrates the extraordinary achievement made by formulating the BCS theory, but also illustrates that mistakes are a natural and healthy part of scientific discourse, and that inapplicable, even incorrect theories can turn out to be interesting and inspiring.
Seminars
Date:
03
March, 2024
Sunday
Hour: 13:15-14:30
The Clore Center for Biological Physics
A Statistical Physics Approach to Bacteria under Strong Perturbations
Prof. Nathalie Q. Balaban | Racah Institute of Physics, The Hebrew University
Statistical physics successfully accounts for phenomena involving a large number of components using a probabilistic approach with predictions for collective properties of the system. While biological cells contain a very large number of interacting components, (proteins, RNA molecules, metabolites, etc.), the cellular network is understood as a particular, highly specific, choice of interactions shaped by evolution, and therefore difficultly amenable to a statistical physics description. Here we show that when a cell encounters an acute but non-lethal stress, its perturbed state can be modelled as random network dynamics. Strong perturbations may therefore reveal the dynamics of the underlying network that are amenable to a statistical physics description. We show that our experimental measurements of the recovery dynamics of bacteria from a strong perturbation can be described in the framework of physical aging in disordered systems (Kaplan Y. et al, Nature 2021). Further experiments on gene expression confirm predictions of the model. The predictive description of cells under and after strong perturbations should lead to new ways to fight bacterial infections, as well as the relapse of cancer after treatment.
Seminars
Date:
25
February, 2024
Sunday
Hour: 13:15-14:30
The Clore Center for Biological Physics
Tails and (boson) peaks in the glassy vibrational density of states
Avraham Moriel | Princeton University - The Department of Mechanical and Aerospace Engineering
Due to their intrinsic nonequilibrium and disordered nature, glasses feature low-frequency, nonphononic vibrations, in addition to phonons. These excess modes generate a peak —the boson peak— in the ratio of the vibrational density of state (VDoS) and Debye’s VDoS of phonons. Yet, the excess vibrations and the boson peak are not fully understood. After presenting the experimental evidence of the boson peak, we will discuss additional universal characteristics of glassy low frequency VDoS obtained through numerical simulations. We will then examine a recently analyzed mean-field model capturing the universal low-frequency glassy VDoS characteristics. Combining reanalyzed experimental data and computer simulations, we will observe that the same mean-field model also captures the origin, nature and properties of the boson peak, yielding a unified physical picture of the low-frequency VDoS spectra of glasses.
FOR THE LATEST UPDATES AND CONTENT ON SOFT MATTER AND BIOLOGICAL PHYSICS AT THE WEIZMANN, VISIT OUR WEBSITE: https://www.biosoftweizmann.com/
Seminars
Date:
11
February, 2024
Sunday
Hour: 13:15-14:30
The Clore Center for Biological Physics
Tunable Architecture of Nematic Disclination Lines
Dr. Hillel Aharoni | department of physics of complex systems
In this talk, I introduce a theoretical framework to tailor three-dimensional defect line architecture in nematic liquid crystals. By drawing an analogy between nematic liquid crystals and magnetostatics, I will show quantitative predictions for the connectivity and shape of defect lines in a nematic confined between two thinly spaced glass substrates. I will demonstrate experimental and numerical verification of these predictions, and identify critical parameters that tune the disclination lines' curvature within an experimental setup, as well as non-dimensional parameters that allow matching experiments and simulations at different length scales. Our system provides both physical insight and powerful tools to induce desired shapes and shape changes of defect lines.
Seminars
Date:
04
February, 2024
Sunday
Hour: 13:15-14:30
The Clore Center for Biological Physics
Multiscale Lattice Modeling and Simulations of Heterogeneous Membranes
Prof. Oded Farago | Biomedical Engineering Department, BGU
Mixtures of lipids and cholesterol (Chol) have been served as simple model systems for studying the biophysical principles governing the formation of liquid ordered raft domains in complex biological systems. These mixtures exhibit a rich phase diagram as a function of temperature and composition. Much of the focus in these studies has been given to the coexistence regime between liquid ordered and liquid disordered phases which resembles rafts floating in the sea of disordered lipids. In the talk, I will present a new lattice model of binary [1] and ternary [2, 3] mixtures containing saturated and unsaturated lipids, and Chol. Simulations of mixtures of thousands of lipids and cholesterol molecules on time scales of hundreds of microseconds show a very good agreement with experimental and atomistic simulation observations across multiple scale, ranging from the local distributions of lipids to the macroscopic phase diagram of such mixtures. Importantly, we find that the liquid ordered domains are highly heterogeneous and consist of Chol-poor hexagonally packed gel-like clusters surrounded by Chol-rich regions at the domain boundaries. The presence of such nano-domains within the liquid ordered regions appears as a characteristic feature of the liquid-ordered state, and makes the interpretation of scattering data ambiguous in mixtures not exhibiting macroscopic phase separation.
Seminars
Date:
28
January, 2024
Sunday
Hour: 13:15-14:15
The Clore Center for Biological Physics
Some organizing principles behind microbial community dynamics
Dr. Amir Erez -Racah | Institute of Physics of the Hebrew University of Jerusalem
Microbial ecosystems, pivotal in global ecological stability, display a diverse array of species, influenced by complex interactions. When considering environments with changing nutrient levels, we have recently suggested an 'early bird' effect. This phenomenon, which results from changing nutrient levels, initial and fast uptake of resources confers an advantage, significantly altering microbial growth dynamics. In serial dilution cultures with varying nutrient levels, this effect leads to shifts in diversity, demonstrating that microbial communities do not adhere to a universal nutrient-diversity relationship. Using a consumer-resource, serial dilution modeling framework, we simulate scenarios of changing nutrient balance, such as variations in phosphorous availability in rainforest soils, to predict a possible lag in ecosystems response near a loss of diversity transition point. Lastly, we explore the notion of 'microbial debt', a form of the early bird advantage, where microbes initially grow rapidly at the cost of later growth or increased mortality. This dynamic, exemplified in both classical chemostat and serial dilution cultures, reveals that such debt can convey an advantage, with varying outcomes on community structure depending on the nature of the trade-off involved. Together, these studies illuminate some organizing principles behind microbial dynamics, balancing growth and survival in changing environments.
Seminars
Date:
21
January, 2024
Sunday
Hour: 13:15-14:15
The Clore Center for Biological Physics
How informative are structures of dna-bound proteins for revealing binding mechanisms inside cells? the case of the Origin of Replication Complex (ORC)
Prof. Naama Barkai,Prof. Naama Barkai | Department of Molecular Genetics- Faculty of Biochemistry
The Origin Recognition Complex (ORC) seeds the replication-fork by binding DNA replication origins, which in budding yeast contain a 17bp DNA motif. High resolution structure of the ORC-DNA complex revealed two base-interacting elements: a disordered basic patch (Orc1-BP4) and an insertion helix (Orc4-IH).
To define ORC elements guiding its DNA binding in-vivo, we mapped genomic locations of 38 designed ORC mutants. We revealed that different ORC elements guide binding at different motifs sites, and these correspond only partially to the structure- described interactions. In particular, we show that disordered basic patches are key for ORC-motif binding in-vivo, including one lacking from the structure. Finally i will discuss how those disordered elements, which insert into the minor-groove can still guide specific ORC-DNA recognition.