相关论文: Optimal flexibility for conformational transitions…
The role of thermal fluctuations on the conformational dynamics of a single closed filament is studied. It is shown that, due to the interaction between charges and bending degrees of freedom, initially circular aggregates may undergo…
We computationally investigate the active transport of tangentially-driven polymers with varying degrees of flexibility and activity in two-dimensional square lattices of obstacles. Tight periodic confinement induces notable conformational…
Biological information processing manifests a huge variety in its complexity and capability among different organisms, which presumably stems from the evolutionary optimization under limited computational resources. Starting from the…
Atomistic simulations were performed on hydrated model lipid multilayers that are representative of the lipid matrix in the outer skin (stratum corneum). We find that cholesterol transfers easily between adjacent leaflets belonging to the…
Bistability is a major mechanism for cellular decision making and usually results from positive feedback in biochemical control systems. Here we show theoretically that bistability between unbound and bound states of adhesion clusters…
We investigate the application of conformable derivatives to model critical phenomena near continuous phase transitions. By incorporating a deformation parameter into the differential structure, we derive unified expressions for…
We consider the rate of transition for a particle between two metastable states coupled to a thermal environment for various magnitudes of the coupling strength, using the recently proposed infrequent metadynamics approach (Tiwary and…
We have analyzed the equilibrium response of chain molecules to stretching. For a homogeneous sequence of monomers, the induced transition from compact globule to extended coil below the $\theta$-temperature is predicted to be sharp. For…
Molecular motors transduce chemical energy obtained from hydrolizing ATP into mechanical work exerted against an external force. We calculate their efficiency at maximum power output for two simple generic models and show that the…
Large language models exhibit sophisticated capabilities, yet understanding how they work internally remains a central challenge. A fundamental obstacle is that training selects for behavior, not circuitry, so many weight configurations can…
Transformers have achieved remarkable success in sequence modeling and beyond but suffer from quadratic computational and memory complexities with respect to the length of the input sequence. Leveraging techniques include sparse and linear…
Combining simulations and theory I study the interplay between bundle elastic degrees of freedom and crosslink binding propensity. By slowly driving bundles into a deformed configuration, and depending on the mechanical stiffness of the…
We study the most probable way an interface moves on a macroscopic scale from an initial to a final position within a fixed time in the context of large deviations for a stochastic microscopic lattice system of Ising spins with Kac…
Flexible mechanical metamaterials possess repeating structural motifs that imbue them with novel, exciting properties including programmability, anomalous elastic moduli and nonlinear and robust response. We address such structures via…
We study a minimal extension of the worm-like chain to describe polypeptides having alpha-helical secondary structure. In this model presence/absence of secondary structure enters as a scalar variable that controls the local chain bending…
We describe a new Hybrid Monte Carlo (HMC) algorithm for dynamical overlap fermions, which improves the rate of topological index changes by adding an additional (intensive) term to the action for the molecular dynamics part of the…
Hybrid systems, which take advantage of low material dimensionality, have great potential for designing nanoscale devices. Quantum dots (QDs) -- a 0D nanostructure -- can be combined with 2D monolayers to achieve success in photovoltaics…
Mixtures of active and passive particles are ubiquitous at the microscale. Many essential microbial processes involve interactions with dead or immotile cells or passive crowders. When passive objects are immersed in active baths, their…
We report dynamic Monte Carlo simulation on conformational transition of H-shaped branched polymers by varying main chain (backbone) and side chain (branch) length. H-shaped polymers in comparison with equivalent linear polymers exhibit a…
The translational order in a three-dimensional lattice pinned by hopping defects is studied. It is suggested that the equilibrium state of the lattice crosses from a glass to a crystal on the rate of hopping. It is argued that such a…