相关论文: TransPath: A Computational Method to Study the Ion…
With the ability to selectively control ionic flux, biological protein ion channels perform a fundamental role in many physiological processes. For practical applications that require the functionality of a biological ion channel, graphene…
Purpose: Cone-beam CT (CBCT) projection images provide anatomical data in real-time over several respiratory cycles, forming a comprehensive picture of tumor movement. We developed and validated a method which uses these projections to…
In machine learning and statistics, probabilistic inference involving multimodal distributions is quite difficult. This is especially true in high dimensional problems, where most existing algorithms cannot easily move from one mode to…
Electron transfer (ET) across molecular chains including an impurity is studied based on a recently improved real-time path integral Monte Carlo (PIMC) approach [J. Chem. Phys. {\bf 121}, 12696 (2004)]. The reduced electronic dynamics is…
We have studied the dynamics of chloride and potassium ions in the interior of the OmpF porin under the influence of an external electric field. From the results of extensive all-atom molecular dynamics simulations of the system we computed…
Constraint-based modeling has been widely used on metabolic networks analysis, such as biosynthetic prediction and flux optimization. The linear constraints, like mass conservation constraint, reversibility constraint, biological capacity…
A new and fast Matlab algorithm for predicting absolute permeability is presented. The developed tool relies on measuring the connectivity of pores in a given three-dimensional (3D) micro-CT rock image. An index of pore connectivity is…
Porous and heterogeneous materials are found in many applications from composites, membranes, chemical reactors, and other engineered materials to biological matter and natural subsurface structures. In this work we propose an integrated…
Recently, it has been suggested that ion channel selectivity filter may exhibit quantum coherence, which may be appropriate to explain ion selection and conduction processes. Potassium channels play a vital role in many physiological…
The field of connectomics faces unprecedented "big data" challenges. To reconstruct neuronal connectivity, automated pixel-level segmentation is required for petabytes of streaming electron microscopy data. Existing algorithms provide…
Quantum phenomena are relevant to the transport of light atoms and molecules through nanoporous two-dimensional (2D) membranes. Indeed, confinement provided by (sub-)nanometer pores enhances quantum effects such as tunneling and zero point…
Markov Chain Monte Carlo (MCMC) algorithms play an important role in statistical inference problems dealing with intractable probability distributions. Recently, many MCMC algorithms such as Hamiltonian Monte Carlo (HMC) and Riemannian…
We propose a new Monte Carlo method for efficiently sampling trajectories with fixed initial and final conditions in a system with discrete degrees of freedom. The method can be applied to any stochastic process with local interactions,…
Pore network modelling has traditionally been used to study displacement processes in idealized porous media related to geological flows, with applications ranging from groundwater hydrology to enhanced oil recovery. Very recently, pore…
{\it De novo} protein sequencing is essential for understanding cellular processes that govern the function of living organisms and all post-translational events and other sequence modifications that occur after a protein has been…
The embedding of complex networks into metric spaces has become a research topic of high interest with a wide variety of proposed methods. Low dimensional hyperbolic spaces offer a natural co-domain for embeddings allowing a roughly uniform…
Ray tracing is increasingly utilized in wireless system simulations to estimate channel paths. In large-scale simulations with complex environments, ray tracing at high resolution can be computationally demanding. To reduce the computation,…
Ion channels play a key role in regulating cell behavior and in electrical signaling. In these settings, polar and charged functional groups -- as well as protein response -- compensate for dehydration in an ion-dependent way, giving rise…
Hybrid Monte Carlo (HMC) generates samples from a prescribed probability distribution in a configuration space by simulating Hamiltonian dynamics, followed by the Metropolis (-Hastings) acceptance/rejection step. Compressible HMC (CHMC)…
We report on a Monte Carlo method that generates one-dimensional trajectories for Bohm's formulation of quantum mechanics that doesn't involve differentiation or integration of any equations of motion. At each time, t=n\delta t…