Physics
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Item Simulation source code for "Myosin and α-actinin regulation of stress fiber contractility under tensile stress"(2023) Ni, Haoran; Ni, Qin; Papoian, Garegin A.; Trache, Andreea; Jiang, Yi; Jiang, YiStress fibers are actomyosin bundles that regulate cellular mechanosensation and force transduction. Connecting to extracellular matrix through focal adhesion complexes, stress fibers actively generate contractile forces with myosin motors and crosslinking proteins. Under external mechanical stimuli such as tensile forces, the stress fiber remodels its architectures to adapt to the external cues, displaying properties of viscoelastic materials. How the structural remodeling of stress fibers is related to the generation of contractile force is not well understood. In this work, we simulate mechanochemical dynamics and force generation of stress fibers using the molecular simulation platform MEDYAN. We model stress fiber as two connecting bipolar bundles attached at the ends to focal adhesion complexes. The simulated stress fibers generate contractile force that is regulated by myosin motors and α-actinin crosslinkers. We find that stress fibers are able to enhance contractility by reducing the distance between actin filaments to increase crosslinker binding, while this structural remodeling ability depends on the crosslinker turnover rate. Under tensile pulling, the stress fiber shows an instantaneous increase of the contractile forces followed by a slow relaxation into a new steady state. While the new steady state contractility after pulling only depends on the overlap between actin bundles, the short term contractility enhancement is sensitive to the tensile pulling distance. We further show that this mechanical response is sensitive to the crosslinker turnover rate. Our results provide insights into the stress fiber mechanics that have significant implications for understanding the cellular adaptation to mechanical signaling.Item Data for "A tug of war between filament treadmilling and myosin induced contractility generates actin ring"(2022-06-23) Ni, Qin; Wagh, Kaustubh; Pathni, Aashli; Ni, Haoran; Vashisht, Vishavdeep; Upadhyaya, Arpita; Papoian, Garegin A.; Upadhyaya, Arpita; Papoian, Garegin A.In most eukaryotic cells, actin filaments assemble into a shell-like actin cortex under the plasma membrane, controlling cellular morphology, mechanics, and signaling. The actin cortex is highly polymorphic, adopting diverse forms such as the ring-like structures found in podosomes, axonal rings, and immune synapses. The biophysical principles that underlie the formation of actin rings and cortices remain unknown. Using a molecular simulation platform, called MEDYAN, we discovered that varying the filament treadmilling rate and myosin concentration induces a finite size phase transition in actomyosin network structures. We found that actomyosin networks condense into clusters at low treadmilling rates or high myosin concentration but form ring-like or cortex-like structures at high treadmilling rates and low myosin concentration. This mechanism is supported by our corroborating experiments on live T cells, which exhibit ring-like actin networks upon activation by stimulatory antibody. Upon disruption of filament treadmilling or enhancement of myosin activity, the pre-existing actin rings are disrupted into actin clusters or collapse towards the network center respectively. Our analyses suggest that the ring-like actin structure is a preferred state of low mechanical energy, which is, importantly, only reachable at sufficiently high treadmilling rates.Item The complexity of simulating quantum physics: dynamics and equilibrium(2021) Deshpande, Abhinav; Gorshkov, Alexey V; Fefferman, Bill; Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Quantum computing is the offspring of quantum mechanics and computer science, two great scientific fields founded in the 20th century. Quantum computing is a relatively young field and is recognized as having the potential to revolutionize science and technology in the coming century. The primary question in this field is essentially to ask which problems are feasible with potential quantum computers and which are not. In this dissertation, we study this question with a physical bent of mind. We apply tools from computer science and mathematical physics to study the complexity of simulating quantum systems. In general, our goal is to identify parameter regimes under which simulating quantum systems is easy (efficiently solvable) or hard (not efficiently solvable). This study leads to an understanding of the features that make certain problems easy or hard to solve. We also get physical insight into the behavior of the system being simulated. In the first part of this dissertation, we study the classical complexity of simulating quantum dynamics. In general, the systems we study transition from being easy to simulate at short times to being harder to simulate at later times. We argue that the transition timescale is a useful measure for various Hamiltonians and is indicative of the physics behind the change in complexity. We illustrate this idea for a specific bosonic system, obtaining a complexity phase diagram that delineates the system into easy or hard for simulation. We also prove that the phase diagram is robust, supporting our statement that the phase diagram is indicative of the underlying physics. In the next part, we study open quantum systems from the point of view of their potential to encode hard computational problems. We study a class of fermionic Hamiltonians subject to Markovian noise described by Lindblad jump operators and illustrate how, sometimes, certain Lindblad operators can induce computational complexity into the problem. Specifically, we show that these operators can implement entangling gates, which can be used for universal quantum computation. We also study a system of bosons with Gaussian initial states subject to photon loss and detected using photon-number-resolving measurements. We show that such systems can remain hard to simulate exactly and retain a relic of the "quantumness" present in the lossless system. Finally, in the last part of this dissertation, we study the complexity of simulating a class of equilibrium states, namely ground states. We give complexity-theoretic evidence to identify two structural properties that can make ground states easier to simulate. These are the existence of a spectral gap and the existence of a classical description of the ground state. Our findings complement and guide efforts in the search for efficient algorithms.Item Data for "Membrane-MEDYAN: Simulating Deformable Vesicles Containing Complex Cytoskeletal Networks"(2021) Ni, Haoran; Papoian, Garegin A.; Papoian, Garegin A.The plasma membrane defines the shape of the cell and plays an indispensable role in bridging intra- and extra-cellular environments. Mechanochemical interactions between plasma membrane and cytoskeleton are vital for cell biomechanics and mechanosensing. A computational model that comprehensively captures the complex, cell-scale cytoskeleton-membrane dynamics is still lacking. In this work, we introduce a triangulated membrane model that accounts for membrane's elastic properties, as well as for membrane-filament steric interactions. The corresponding force-field was incorporated into the active biological matter simulation platform, MEDYAN ("Mechanochemical Dynamics of Active Networks"). Simulations using the new model shed light on how actin filament bundling affects generation of tubular membrane protrusions. In particular, we used membrane-MEDYAN simulations to investigate protrusion initiation and dynamics while varying geometries of filament bundles, membrane rigidities and local G-Actin concentrations. We found that bundles' protrusion propensities sensitively depend on the synergy between bundle thickness and inclination angle at which the bundle approaches the membrane. The new model paves the way for simulations of biological systems involving intricate membrane-cytoskeleton interactions, such as occurring at the leading edge and the cortex, eventually helping to uncover the fundamental principles underlying the active matter organization in the vicinity of the membrane.Item Theoretical Studies of the Workings of Processive Molecular Motors(2017) Vu, Huong Thuy; Thirumalai, Devarajan; Biophysics (BIPH); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Processive molecular motors, such as kinesins, myosins and helicases, take multiple discrete steps on linear polar tracks such as microtubules, filamentous actin, and DNA/RNA substrates. Insights into the mechanisms and functions of this important class of biological motors have been obtained through observations from single-molecule experiments and structural studies. Such information includes the distribution of n, the number of steps motors take before dissociating, and v, the motor velocity, in the presence and absence of an external resistive force from single molecule experiments; and different structures of different states of motors at different conditions. Based on those available data, this thesis focuses on using both analytical and computational theoretical tools to investigate the workings of processive motors. Two examples of processive motors considered here are kinesins that walk on microtubules while transporting vesicles, and helicases which translocate on DNA/RNA substrate while unwinding the helix substrate. New physical principles and predictions related to their motility emerge from the proposed theories. The most significant results reported in this thesis are: Exact and approximate equations for velocity distribution, P(v), and runlength distribution, P(n), have been derived. Application of the theory to kinesins shows that P(v) is non-Gaussian and bimodal at high resistive forces. This unexpected behavior is a consequence of the discrete spacing between the alpha/beta tubulins, the building blocks of microtubule. In the case of helicases, we demonstrate that P(v) of typical helicases T7 and T4 shows signatures of heterogeneity, inferred from large variations in the velocity from molecule to molecule. The theory is used to propose experiments in order to distinguish between different physical basis for heterogeneity. We generated a one-microsecond atomic simulation trajectory capturing the docking process of the neck-linker, a crucial element deemed to be important in the motility of Kinesin-1. The conformational change in the neck linker is important in the force generation in this type of motor. The simulations revealed new conformations of the neck-linker that have not been noted in previous structural studies of Kinesin-1, but which are demonstrated to be relevant to another superfamily member, Kinesin-5. By comparing the simulation results with currently available data, we suggest that the two superfamilies might actually share more similarities in the neck-linker docking process than previously thought.Item Modeling and simulation of organic molecular clusters and overlayers on solid surfaces(2011) Liu, Qiang; Weeks, John D; Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Driven by the rapid development of experimental methods and technology, nano scale physics and chemistry has become more and more important and practicable to study. Monolayers of organic molecules have been studied a lot recently because of many potential applications, such as organic photovoltaic devices (OPV) or organic Liquid Electric Diodes (OLED). It is important to understand and interpret these new experimental advances. At molecular scales, Monte Carlo (MC) simulations and molecular dynamics (MD) are two important methods in computational chemistry and materials science. This dissertation will use these simulation methods along with statistical mechanical theory to study the behavior of single monolayers of organic molecules on solid surfaces. First we give a brief introduction to two dimensional molecular systems. Different from bulk system or single molecules, 2D systems have many unique properties, and attract much experimental and theoretical research attention. Some common methods in experimental and theoretical studies are reviewed. After introducing the properties and experimental results of ACA/Ag(111), we build a lattice gas model and run Monte Carlo simulations to help interpret the experiments. The Pair approximation, a generalization of mean-field theory, is used to calculate the global phase diagrams and put our model into the more general class of spin-1 Ising models. The pair approximation can be used for modeling various monolayer organic molecular systems which correspond to different regions of the parameter space. Then we studied the C60/ZnPc/Ag(111) system, using molecular dynamic simulations. The C60 molecules form unusual chain structures instead of the close packed islands seen on metal surfaces, and we try to provide a theoretical explanation. Finally we use a density functional theory software to calculate the electronic structures of the C60/ZnPc/Ag(111) systems. This calculation predicts a 0.4e charge transfer from substrate to C60 molecule, which we believe is important for the C60 interactions on these surfaces. In general this thesis studies the behavior of organic monolayers and bilayers on metal substrates. This basic work could help us to understand general 2-D system dynamics and electronic properties, and may help us to find new interesting systems with special properties and applications.Item Conformational Sampling and Calculation of Molecular Free Energy Using Superposition Approximations(2011) Somani, Sandeep; Gilson, Michael K; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The superposition approximations (SAs), first proposed in the distribution function theories of liquids, are a family of approximations to a multivariate probability distribution function (pdf) in terms of its lower order marginal pdfs. In this talk, we first present the relationship between various forms of SA, the measurement of correlation via mutual information, and approximations to the entropy of the full pdf via truncations of the Mutual Information Expansion. Next, based on the SAs, a novel framework to construct computationally tractable approximations to the N-dimensional Boltzmann conformational distribution of molecule in terms of its low order marginal pdfs is presented. The marginal pdfs are obtained as normalized histograms of internal coordinates of a set of Boltzmann distributed conformations obtained by molecular dynamics (MD) simulation. We evaluate the accuracy of these approximate distributions constructed from marginal pdfs of order L <=3 for small molecules (<= 52 atoms) by using a novel conformational sampling algorithm to sample from them and comparing the samples with the original MD conformations used to populate the pdfs. We find that the triplet (L=3) level approximation has high conformational overlap with the physical Boltzmann distribution, and significantly better than that for the singlet (L=1) or doublet (L=2) level approximations. The results shed light on the relative importance of correlations of different orders. The singlet (L=1) and doublet (L=2) level approximate distributions are then used to define reference systems with known free energies, and then to compute the physical free energy of molecules using the reference system approach. Free energies are computed for small peptides as test molecules, and it is found that the convergence of the free energy estimate using a doublet reference is dramatically faster than with the singlet reference, consistent with greater overlap of the doublet reference system with the physical system. Potential further developments and practical applications are discussed.Item Trinity: A Unified Treatment of Turbulence, Transport, and Heating in Magnetized Plasmas(2009) Barnes, Michael; Dorland, William; Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)To faithfully simulate ITER and other modern fusion devices, one must resolve electron and ion fluctuation scales in a five-dimensional phase space and time. Simultaneously, one must account for the interaction of this turbulence with the slow evolution of the large-scale plasma profiles. Because of the enormous range of scales involved and the high dimensionality of the problem, resolved first-principles global simulations are very challenging using conventional (brute force) techniques. In this thesis, the problem of resolving turbulence is addressed by developing velocity space resolution diagnostics and an adaptive collisionality that allow for the confident simulation of velocity space dynamics using the approximate minimal necessary dissipation. With regard to the wide range of scales, a new approach has been developed in which turbulence calculations from multiple gyrokinetic flux tube simulations are coupled together using transport equations to obtain self-consistent, steady-state background profiles and corresponding turbulent fluxes and heating. This approach is embodied in a new code, Trinity, which is capable of evolving equilibrium profiles for multiple species, including electromagnetic effects and realistic magnetic geometry, at a fraction of the cost of conventional global simulations. Furthermore, an advanced model physical collision operator for gyrokinetics has been derived and implemented, allowing for the study of collisional turbulent heating, which has not been extensively studied. To demonstrate the utility of the coupled flux tube approach, preliminary results from Trinity simulations of the core of an ITER plasma are presented.