Related papers: Multiscale modelling of bionano interface
Molecular dynamics simulations provide theoretical insight into the microscopic behavior of materials in condensed phase and, as a predictive tool, enable computational design of new compounds. However, because of the large temporal and…
Long-term biomolecular dynamics are critical for understanding key evolutionary transformations in molecular systems. However, capturing these processes requires extended simulation timescales that often exceed the practical limits of…
The excimer formation dynamics of pyrene-labeled molecules in lipid bilayers depends on molecular motion over distances of the order of 1-2 nm. From the concentration dependence of the excimer photoemission curve, it is possible to derive a…
An important challenge in robotics is understanding the interactions between robots and deformable terrains that consist of granular material. Granular flows and their interactions with rigid bodies still pose several open questions. A…
We describe a complete methodology to bridge the scales between nanoscale Molecular Dynamics and (micrometer) mesoscale Monte Carlo simulations in lipid membranes and vesicles undergoing phase separation, in which curving molecular species…
Polymer properties are inherently multi-scale in nature, where delicate local interaction details play a key role in describing their global conformational behavior. In this context, deriving coarse-grained (CG) multi-scale models for…
Discrete energy minimization is a ubiquitous task in computer vision, yet is NP-hard in most cases. In this work we propose a multiscale framework for coping with the NP-hardness of discrete optimization. Our approach utilizes algebraic…
Protein structure prediction (PSP) is computationally a very challenging problem. The challenge largely comes from the fact that the energy function that needs to be minimised in order to obtain the native structure of a given protein is…
Lipid bilayers often form high-curvature configurations due to self-assembly conditions or certain biological processes. However, particle-based simulations of lipid membranes are predominantly of flat lipid membranes because planar…
The cryogenic buffer gas beam (CBGB) is an important tool in the study of cold and ultracold molecules. While there are known techniques to enhance desired beam properties, such as high flux, low velocity, or reduced divergence, they have…
Heterogeneous molecular entities and their interactions, commonly depicted as a network, are crucial for advancing our systems-level understanding of biology. With recent advancements in high-throughput data generation and a significant…
Mesoscopic simulations of hydrocarbon flow in source shales are challenging, in part due to the heterogeneous shale pores with sizes ranging from a few nanometers to a few micrometers. Additionally, the sub-continuum fluid-fluid and…
This paper presents a novel approach for accelerating n-body simulations by integrating a physics-informed graph neural networks (GNN) with traditional numerical methods. Our method implements a leapfrog-based simulation engine to generate…
Developing effective coarse grained (CG) approach is a promising way for studying dynamics on large size networks. In the present work, we have proposed a strength-based CG (\sCG) method to study critical phenomena of the Potts model on…
Early detection of cancer is essential for timely diagnosis and improved patient outcomes. Among emerging technologies, intra-body nanoscale communication offers an innovative solution to identify molecular cues within the human…
The conformational behavior of a coarse-grained finite polymer chain near an attractive spherical surface was investigated by means of multicanonical Monte Carlo computer simulations. In a detailed analysis of canonical equilibrium data…
Machine-learned coarse-grained (CG) models often suffer from noisy training data, limiting their accuracy and transferability. We propose a method to generate low-noise training data based on the potential of mean force by constraining CG…
We present the state-of-the-art theoretical modeling, molecular simulation, and coarse-graining strategies for the transport of gases and liquids in nanoporous materials (pore size 1-100 nm). Special emphasis is placed on the transport of…
We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic Langevin molecular dynamics (MD) with a mesoscopic lattice Boltzmann (LB) method for the…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…