Magnetic shape memory alloys (MSM alloys), a new kind of smart materials, have become a potential candidate in many engineering fields. MSMs have the advantage of bearing a huge strain, much larger than other materials. In addition, they also have fast response. These characteristics make MSM a good choice in micro engineering. However, MSMs display the obvious hysteresis phenomenon of nonlinea...

In a series of papers, Robins and colleagues describe inverse probability of treatment weighted (IPTW) estimation in marginal structural models (MSMs), a method of causal analysis of longitudinal data based on counterfactual principles. This family of statistical techniques is similar in concept to weighting of survey data, except that the weights are estimated using study data rather than defi...

We consider time-continuous, reversible Markov processes on large or continuous state space. For a practical analysis of such processes it is often necessary to construct low dimensional approximations, like Markov State Models (MSM). MSM have been used for this purpose in several applications, particularly in molecular dynamics, see [16] for an example. One of the main goals of MSMs is the cor...

The first cases of acquired immunodeficiency syndrome (AIDS) were reported in the United States in the spring of 1981. By 1983 the human immunodeficiency virus (HIV), the virus that causes AIDS, had been isolated. Early in the U.S. HIV/AIDS pandemic, the role of substance abuse in the spread of AIDS was clearly established. Injection drug use (IDU) was identified as a direct route of HIV infect...

Computer simulations can complement experiments by providing insight into molecular kinetics with atomic resolution. Unfortunately, even the most powerful supercomputers can only simulate small systems for short timescales, leaving modeling of most biologically relevant systems and timescales intractable. In this work, however, we show that molecular simulations driven by adaptive sampling of n...

Because standard molecular dynamics (MD) simulations are unable to access time scales of interest in complex biomolecular systems, it is common to "stitch together" information from multiple shorter trajectories using approximate Markov state model (MSM) analysis. However, MSMs may require significant tuning and can yield biased results. Here, by analyzing some of the longest protein MD data se...

Molecular dynamics with explicit solvent is favored for its ability to more correctly simulate aqueous biological processes and has become routine thanks to increasingly powerful computational resources. However, analysis techniques including Markov state models (MSMs) ignore solvent atoms and focus solely on solute coordinates despite solvent being implicated in myriad biological phenomena. We...

In the increasingly complex prosthetic limbs for upper extremity amputees, more mechanical degrees of freedom are combined with various neural commands to produce versatile human-like movements. Development, testing, and fitting of such neural prosthetic systems and training patients to control them effectively are complex processes that cannot be performed efficiently or safely by ad hoc and t...

We propose a discrete transition-based reweighting analysis method (dTRAM) for analyzing configuration-space-discretized simulation trajectories produced at different thermodynamic states (temperatures, Hamiltonians, etc.) dTRAM provides maximum-likelihood estimates of stationary quantities (probabilities, free energies, expectation values) at any thermodynamic state. In contrast to the weighte...

Introduction (aim) Nigeria currently has one of the highest HIV and AIDS epidemic burden worldwide. Prevalence among key populations is currently, 34.1% (brothel-based sex workers), 21.95 (non-brothel-based), 37.6% (MSMs) and 9.3% for IDUs respectively. A huge gaps exists in the national response to key populations as a result of socio-cultural barriers and unfavorable political and legislative...