相关论文: Rigid Base Biasing in Molecular Dynamics enables e…

The experimental measurement of correlation functions and critical exponents in disordered systems is key to testing renormalization group (RG) predictions. We mechanically unzip single DNA hairpins with optical tweezers, an experimental…

While the autonomous assembly of hard nanoparticles with different shapes has been studied extensively both in experiment and simulations, little is known about systems where particle shape can be dynamically altered. DNA origami…

We study DNA self-assembly and DNA computation using a coarse-grained DNA model within the directional dynamic bonding framework {[}C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012){]}. In our model, a single nucleotide or domain is…

Recent single-molecule pulling experiments have shown how it is possible to manipulate RNA molecules using optical tweezers force microscopy. We investigate a minimal model for the experimental setup which includes a RNA molecule connected…

Simulating large-scale articulated assemblies poses a significant challenge due to the numerical stiffness and geometric complexity of jointed structures. Conventional rigid body solvers struggle with the high nonlinearity induced by…

Reduced-order simulation is an emerging method for accelerating physical simulations with high DOFs, and recently developed neural-network-based methods with nonlinear subspaces have been proven effective in diverse applications as more…

The rotating nuclei represent one of most interesting subjects for theoretical and experimental studies. They open a new dimension of nuclear landscape, namely, spin direction. Contrary to the majority of nuclear systems, their properties…

Many important challenges in science and technology can be cast as optimization problems. When viewed in a statistical physics framework, these can be tackled by simulated annealing, where a gradual cooling procedure helps search for…

Deoxyribonucleic acid (DNA) has shown great promise in enabling computational applications, most notably in the fields of DNA digital data storage and DNA computing. Information is encoded as DNA strands, which will naturally bind in…

In many areas of engineering, nonlinear numerical analysis is playing an increasingly important role in supporting the design and monitoring of structures. Whilst increasing computer resources have made such formerly prohibitive analyses…

Here we use large-scale molecular dynamics (MD) simulations of the high-rate deformation of nanocrystalline tantalum to investigate the processes associated with plastic deformation for strains up to 100%. We use initial atomic…

Atomistic simulations of the molecular dynamics/statics kind are regularly used to study small scale plasticity. Contemporary simulations are performed with tens to hundreds of millions of atoms, with snapshots of these configurations…

Particle accelerators play a pivotal role in advancing scientific research, yet optimizing beamline configurations to maximize particle transmission remains a labor-intensive task requiring expert intervention. In this work, we introduce…

Bending of DNA from a straight rod to a circular form in presence of any of the mono-, di-, tri- or tetravalent counterions has been simulated in strong Coulomb coupling environment employing a previously developed energy minimization…

The process of RNA base fraying (i.e. the transient opening of the termini of a helix) is involved in many aspects of RNA dynamics. We here use molecular dynamics simulations and Markov state models to characterize the kinetics of RNA…

Atomic-resolution scanning transmission electron microscopy (STEM) characterization requires precise tilting of the specimen to high symmetric zone axis, which is usually processed in reciprocal space by following the diffraction patterns.…

DNA cyclization is a powerful technique to gain insight into the nature of DNA bending. The worm-like chain model provides a good description of small to moderate bending fluctuations, but some experiments on strongly-bent shorter molecules…

A novel approach for structure alignment is presented, where the key ingredients are: (1) An error function formulation of the problem simultaneously in terms of binary (Potts) assignment variables and real-valued atomic coordinates. (2)…

Nucleic acids, like DNA and RNA, are molecules that are present in any life form. Their most notable function is to encode biological information. Why then would a physicist be interested in these molecules? As we will see, DNA is an…

We propose a scheme to calibrate the internal parameters of a quantum annealer to obtain well-approximated samples for training a restricted Boltzmann machine (RBM). Empirically, samples from quantum annealers obey the Boltzmann…