相关论文: A new configurational bias scheme for sampling sup…

Somatic mutations in cancer can be viewed as a mixture distribution of several mutational signatures, which can be inferred using non-negative matrix factorization (NMF). Mutational signatures have previously been parametrized using either…

The simulated self-assembly of molecular building blocks into functional complexes is a key area of study in computational biology and materials science. Self-assembly simulations of proteins using physically-motivated potentials for…

Generating large ensembles of candidate conformations is standard for improving biomolecular structure prediction. Yet aimless sampling is inefficient and costly, producing many redundant conformations with limited diversity, so additional…

The problem of learning the structure of a high dimensional graphical model from data has received considerable attention in recent years. In many applications such as sensor networks and proteomics it is often expensive to obtain samples…

In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…

Certain sequences of peptoid polymers (synthetic analogs of peptides) assemble into bilayer nanosheets via a nonequilibrium assembly pathway of adsorption, compression, and collapse at an air-water interface. As with other large-scale…

We study the conformational behavior of a polymer adsorbed at an attractive nanostring and construct the complete structural phase diagram in dependence of the binding strength and effective thickness of the string. For this purpose, Monte…

Numerical integration and emulation are fundamental topics across scientific fields. We propose novel adaptive quadrature schemes based on an active learning procedure. We consider an interpolative approach for building a surrogate…

The increased energy and power density required in modern electronics poses a challenge for designing new dielectric polymer materials with high energy density while maintaining low loss at high applied electric fields. Recently, an…

The assembly of proteins in membranes plays a key role in many crucial cellular pathways. Despite their importance, characterizing transmembrane assembly remains challenging for experiments and simulations. Equilibrium molecular dynamics…

One of the most important tasks in understanding the complex spatial organization of the genome consists in extracting information about this spatial organization, the function and structure of chromatin topological domains from existing…

A simple model of a circularly closed dsDNA in a poor solvent is considered as an example of a semi-flexible polymer with self-attraction. To find the ground states, the conformational energy is computed as a sum of the bending and…

A wide variety of numerical methods are evaluated and compared for solving the stochastic differential equations encountered in molecular dynamics. The methods are based on the application of deterministic impulses, drifts, and Brownian…

We present an analytically solvable model for self-assembly of a molecular complex on a filament. The process is driven by a seed molecule that undergoes facilitated diffusion, which is a search strategy that combines diffusion in…

Higher-order motif structures and multi-vertex interactions are becoming increasingly important in studies that aim to improve our understanding of functionalities and evolution patterns of networks. To elucidate the role of higher-order…

High read depth can be used to assemble short sequence repeats. The existing genome assemblers fail in repetitive regions of longer than average read. I propose a new algorithm for a DNA assembly which uses the relative frequency of reads…

The functionality of catalysts, enzymes, and supramolecular assemblies emerges not from individual molecules alone, but from the subtle interplay between multiple components arranged in complex systems. Designing such systems is a grand…

A computational method is presented which is capable to obtain low lying energy structures of topological amorphous systems. The method merges a differential mutation genetic algorithm with simulated annealing. This is done by incorporating…

We construct the complete structural phase diagram of polymer adsorption at substrates with attractive stripe-like patterns in the parameter space spanned by the adsorption affinity of the stripes and temperature. Results were obtained by…

We systematically explore the self-assembly of semi-flexible polymers in deformable spherical confinement across a wide regime of chain stiffness, contour lengths and packing fractions by means of coarse-grained molecular dynamics…