Related papers: Precision and Stability Issues in VBL, the Virtual…

In this perspective, we discuss where and how accounting for electronic many-body polarization affects the accuracy of classical molecular dynamics simulations of biomolecules.While the effects of electronic polarization are highly…

The possibility that evolutionary forces -- together with a few fundamental factors such as thermodynamic constraints, specific computational features enabling information processing, and ecological processes -- might constrain the logic of…

The importance of stochasticity within biological systems has been shown repeatedly during the last years and has raised the need for efficient stochastic tools. We present SABRE, a tool for stochastic analysis of biochemical reaction…

Molecular dynamics simulations allow to study the structure and dynamics of single biomolecules in microscopic detail. However, many processes occur on time scales beyond the reach of fully atomistic simulations and require coarse-grained…

Machine learning tasks involving biomedical signals frequently grapple with issues such as limited data availability, imbalanced datasets, labeling complexities, and the interference of measurement noise. These challenges often hinder the…

Understanding the physics of beam-plasma systems is of great importance for a large number of astrophysical systems. Recently the validity of particle-in-cell simulations of these systems has been questioned by Shalaby et al. (2017) We…

Organogenesis is a tightly regulated process that has been studied experimentally for decades. Computational models can help to integrate available knowledge and to better understand the underlying regulatory logic. We are currently…

The behavior of some stochastic chemical reaction networks is largely unaffected by slight inaccuracies in reaction rates. We formalize the robustness of state probabilities to reaction rate deviations, and describe a formal connection…

Efficient simulation of quantum mechanical problems can be performed in a quantum computer where the interactions of qubits lead to the realization of various problems possessing quantum nature. Spin-Boson Model (SBM) is one of the striking…

Despite the impressive advances in biological imaging, no imaging modality today generates, in a comprehensive manner, high-resolution images of crowded molecules working deep inside the living cell in real time. In this paper, instead of…

Dynamical systems modeling, particularly via systems of ordinary differential equations, has been used to effectively capture the temporal behavior of different biochemical components in signal transduction networks. Despite the recent…

A formalism is developed which describes the extent to which stochastic oscillations in biochemical models are synchronised. It is based on the calculation of the complex coherence function within the linear noise approximation. The method…

Computer simulations have become a very powerful tool for scientific research. In order to facilitate research in computational biology, the BioDynaMo project aims at a general platform for biological computer simulations, which should be…

Simulating response properties of molecules is crucial for interpreting experimental spectroscopies and accelerating materials design. However, it remains a long-standing computational challenge for electronic structure methods on classical…

In this paper we have investigated, through computer simulations, dislocation nucleation and dislocation dynamics in a heterostructure system with the lattice-mismatch interface, i.e. a system with internal strain. In particular, we have…

Cellular bioelectricity describes the biological phenomenon in which cells in living tissue generate and maintain patterns of voltage gradients induced by differing concentrations of charged ions. A growing body of research suggests that…

Since its foundations, more than one hundred years ago, the field of structural biology has strived to understand and analyze the properties of molecules and their interactions by studying the structure that they take in 3D space. However,…

We introduce RuleVis, a web-based application for defining and editing "correct-by-construction" executable rules that model biochemical functionality, which can be used to simulate the behavior of protein-protein interaction networks and…

Diffusion involving atom transport from one location to another governs many important processes and behaviors such as precipitation and phase nucleation. Local chemical complexity in compositionally complex alloys poses challenges for…

Computational experiments have become essential for scientific discovery, allowing researchers to test hypotheses, analyze complex datasets, and validate findings. However, as computational experiments grow in scale and complexity, ensuring…