相关论文: Sampling of conformational ensemble for virtual sc…

This paper devises a novel lowest-order conforming virtual element method (VEM) for planar linear elasticity with the pure displacement/traction boundary condition. The main trick is to view a generic polygon $K$ as a new one…

Model ensembling is a well-established technique for improving the performance of machine learning models. Conventionally, this involves averaging the output distributions of multiple models and selecting the most probable label. This idea…

Molecular dynamics is a powerful tool for studying the thermodynamics and kinetics of complex molecular events. However, these simulations can rarely sample the required time scales in practice. Transition path sampling overcomes this…

We apply the "weighted ensemble" (WE) simulation strategy, previously employed in the context of molecular dynamics simulations, to a series of systems-biology models that range in complexity from one-dimensional to a system with 354…

The dynamic of complex ordering systems with active rotational degrees of freedom exemplified by protein self-assembly is explored using a machine learning workflow that combines deep learning-based semantic segmentation and rotationally…

This paper presents a molecular mechanics study using a molecular dynamics software (NAMD) coupled to virtual reality (VR) techniques for intuitive Bio-NanoRobotic prototyping. Using simulated Bio-Nano environments in VR, the operator can…

Collaborative Representation Classification (CRC) for face recognition attracts a lot attention recently due to its good recognition performance and fast speed. Compared to Sparse Representation Classification (SRC), CRC achieves a…

Molecular dynamics (MD) simulation has long been the principal computational tool for exploring protein conformational landscapes and dynamics, but its application is limited by high computational cost. We present ProTDyn, a foundation…

Selecting an effective docking algorithm is highly context-dependent, and no single method performs reliably across structural, chemical, or protocol regimes. We introduce MolAS, a lightweight algorithm selection system that predicts…

This paper presents a new C++ framework, DELPHES, performing a fast multipurpose detector response simulation. The simulation includes a tracking system, embedded into a magnetic field, calorimeters and a muon system, and possible very…

Coarse-grained (CG) models parameterized using atomistic reference data, i.e., 'bottom up' CG models, have proven useful in the study of biomolecules and other soft matter. However, the construction of highly accurate, low resolution CG…

One of the key limitations of Molecular Dynamics simulations is the computational intractability of sampling protein conformational landscapes associated with either large system size or long timescales. To overcome this bottleneck, we…

The accurate sampling of protein dynamics is an ongoing challenge despite the utilization of High-Performance Computers (HPC) systems. Utilizing only "brute force" MD simulations requires an unacceptably long time to solution. Adaptive…

We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a…

We describe different Bayesian ensemble refinement methods, examine their interrelation, and discuss their practical application. With ensemble refinement, the properties of dynamic and partially disordered (bio)molecular structures can be…

Continuum robots, known for their high flexibility and adaptability, offer immense potential for applications such as medical surgery, confined-space inspections, and wearable devices. However, their non-linear elastic nature and complex…

A novel compute intensification methodology to the construction of low-dimensional, high-fidelity "compact" kinetic models for NOX formation is designed and demonstrated. The method adapts the data intensive Machine Learned Optimization of…

The proper biological functioning of proteins often relies on the occurrence of coordinated fluctuations around their native structure, or of wider and sometimes highly elaborated motions. Coarse-grained elastic-network descriptions are…

Although RNAs play many cellular functions little is known about the dynamics and thermodynamics of these molecules. In principle, all-atom molecular dynamics simulations can investigate these issues, but with current computer facilities,…

The latest biological findings observe that the traditional motionless 'lock-and-key' theory is not generally applicable because the receptor and ligand are constantly moving. Nonetheless, remarkable changes in associated atomic sites and…