Related papers: A dynamic intermediate state limits the folding ra…
Accurate protein function prediction requires integrating heterogeneous intrinsic signals (e.g., sequence and structure) with noisy extrinsic contexts (e.g., protein-protein interactions and GO term annotations). However, two key challenges…
With the help of lattice Monte Carlo modelling of heteropolymers, we show that the necessary condition for a protein to fold on short call is to proceed through partially folded intermediates. These elementary structures are formed at an…
Morphologies in phase separating systems can significantly influence the final properties of materials. We present extensive Monte Carlo (MC) simulation results on the segregation kinetics of the critical binary (AB) mixture with a fraction…
We have developed a new simulation method to estimate the distance between the native state and the first transition state, and the distance between the intermediate state and the second transition state of a protein which mechanically…
We study the indentation of a free-standing lipid membrane suspended over a nanopore on a hydrophobic substrate by means of molecular dynamics simulations. We find that in the course of indentation, the membrane bends at the point of…
A dynamic phase transition (DPT) with respect to the period P of an applied alternating magnetic field has been observed previously in numerical simulations of magnetic systems. However, experimental evidence for this DPT has thus far been…
We consider the statistical mechanics of a full set of two-dimensional protein-like heteropolymers, whose thermodynamics is characterized by the coil-to-globular ($T_\theta$) and the folding ($T_f$) transition temperatures. For our model,…
Transition metal dichalcogenides (TMDs) display a rich variety of instabilities such as spin and charge orders, Ising superconductivity and topological properties. Their physical properties can be controlled by doping in electric…
A simple statistical mechanical model proposed by Wako and Sait$\hat{\rm o}$ has explained the aspects of protein folding surprisingly well. This model was systematically applied to multiple proteins by Mu$\tilde{\rm n}$oz and Eaton and has…
Understanding the protein folding process is an outstanding issue in biophysics; recent developments in molecular dynamics simulation have provided insights into this phenomenon. However, the large freedom of atomic motion hinders the…
We consider the dynamics of a rigid filament in a motor protein assay under external loading. The motor proteins are modeled as active harmonic linkers with tail ends immobilized on a substrate. Their heads attach to the filament…
In the framework of a lattice-model study of protein folding, we investigate the interplay between designability, thermodynamic stability, and kinetics. To be ``protein-like'', heteropolymers must be thermodynamically stable, stable against…
Biopolymers serve as one-dimensional tracks on which motor proteins move to perform their biological roles. Motor protein phenomena have inspired theoretical models of one-dimensional transport, crowding, and jamming. Experiments studying…
Many enhanced sampling methods, such as Umbrella Sampling, Metadynamics or Variationally Enhanced Sampling, rely on the identification of appropriate collective variables. For proteins, even small ones, finding appropriate collective…
We investigate the nonequilibrium dynamics of semiflexible polymers driven by motor proteins (MPs) in two-dimensional motility assays under harmonic confinement. Using a coarse-grained agent-based model that incorporates stochastic motor…
Boron phosphide (BP) is a (super)hard semiconductor constituted of light elements, which is promising for high demand applications at extreme conditions. The behavior of BP at high temperatures and pressures is of special interest but is…
Developing accurate and efficient coarse-grained representations of proteins is crucial for understanding their folding, function, and interactions over extended timescales. Our methodology involves simulating proteins with molecular…
We investigate proteins within heterogeneous cell membranes where non-equilibrium phenomena arises from spatial variations in concentration and temperature. We develop simulation methods building on non-equilibrium statistical mechanics to…
In this work, we develop first near-complete 3D models for NTD-hXPB - the N-terminal protein domain of the human transcription factor XPB. The results are very significant as NTD-hXPB plays a critical role in the synthesis of proteins…
We describe the results obtained from an improved model for protein folding. We find that a good agreement with the native structure of a 46 residue long, five-letter protein segment is obtained by carefully tuning the parameters of the…