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Ultrasonic guided waves offer a convenient and practical approach to structural health monitoring and non-destructive evaluation. A key property of guided waves is the fully-defined relationship between central frequency and propagation…
The Hamiltonian Monte Carlo (HMC) algorithm is a powerful Markov Chain Monte Carlo (MCMC) method that uses Hamiltonian dynamics to generate samples from a target distribution. To fully exploit its potential, we must understand how…
We study the effect of intracellular ion diffusion on ionic currents permeating through the cell membrane. Ion flux across the cell membrane is mediated by special proteins forming specific channels. The structure of potassium channels have…
We describe CPMC-Lab, a Matlab program for the constrained-path and phaseless auxiliary-field Monte Carlo methods. These methods have allowed applications ranging from the study of strongly correlated models, such as the Hubbard model, to…
An important open problem in robotic planning is the autonomous generation of 3D inspection paths -- that is, planning the best path to move a robot along in order to inspect a target structure. We recently suggested a new method for…
In tissues, cells in direct physical contact with each other can exchange ions or molecules via protein clusters called gap junctions that form channels across the membranes of adjacent cells. Here, we use a simplified biomimetic approach,…
For many membrane proteins the determination of their topology remains a challenge for methods like X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy. Electron paramagnetic resonance (EPR) spectroscopy has evolved as…
A new method, based on the simulated annealing algorithm and aimed at the inverse problem in the analysis of intergalactic (interstellar) complex spectra of hydrogen and metal lines, is presented. We consider the process of line formation…
The task of accurately locating fluid phase boundaries by means of computer simulation is hampered by problems associated with sampling both coexisting phases in a single simulation run. We explain the physical background to these problems…
We use Brownian dynamics simulations to study the permeation properties of a generic electrostatic model of a biological ion channel as a function of the fixed charge $Q_f$ at its selectivity filter. We reconcile the recently-discovered…
A physical model for a structured tetrameric pore is studied. The pore is modeled as a device composed of four subunits, each one exhibiting two possible states (open and closed). The pore is located within a membrane that separates two…
A framework for topology optimization of cooling channels is proposed, which paves the way towards automated design of additively-manufactured cooling channels, required in applications such as the efficient heat management of die casting…
Ionic Coulomb blockade is one of the mesoscopic effects in ion transport revealing the quantized nature of ionic charges, which is of crucial importance to our understanding of the sub-continuum transport in nanofluidics and the mechanism…
Despite the simplicity of its molecular unit, water is a challenging system because of its uniquely rich polymorphism and predicted but yet unconfirmed features. Introducing a novel space of generalized coordinates that capture changes in…
Rare event sampling algorithms are essential for understanding processes that occur infrequently on the molecular scale, yet they are important for the long-time dynamics of complex molecular systems. One of these algorithms, transition…
Advanced algorithms are necessary to obtain faster-than-real-time dynamic simulations in a number of different physical problems that are characterized by widely disparate time scales. Recent advanced dynamic Monte Carlo algorithms that…
Fluid flow through intricate confining geometries often exhibits complex behaviors, certainly in porous materials, e.g. in groundwater flows or the operation of filtration devices and porous catalysts. However, it has remained extremely…
Pore structures and gas transport properties in porous separators for polymer electrolyte fuel cells are evaluated both experimentally and through simulations. In the experiments, the gas permeabilities of two porous samples, a conventional…
Insertion Sequences (ISs) are small DNA segments that have the ability of moving themselves into genomes. These types of mobile genetic elements (MGEs) seem to play an essential role in genomes rearrangements and evolution of prokaryotic…
In this work, a machine learning approach for identifying the multi-omics metabolic regulatory control circuits inside the pathways is described. Therefore, the identification of bacterial metabolic pathways that are more regulated than…