With the advent of faster computer processors and especially graphics processing units
(GPUs) over the last few decades, the use of data-intensive machine learning (ML) and …

Regulatory protein access to the DNA duplex 'interior'depends on local DNA
'breathing'fluctuations, and the most fundamental of these are thermally-driven base …

The dynamics of polymer melts at the crossover between unentangled and entangled
regimes is formalized here through an extension of the Cooperative Dynamics Generalized …

Macromolecular liquids display short-time anomalous behaviors in disagreement with
conventional single-molecule mean-field theories. In this study, we analyze the behavior of …

It has been established that Terahertz (THz) band signals can interact with biomolecules
through resonant modes. Specifically, of interest here, protein activation. Our research goal …

Molecular Dynamics (MD) simulations of proteins implicitly contain the information
connecting the atomistic molecular structure and proteins' biologically relevant motion …

It has been established that interfacing Terahertz (THz) band signals with protein molecules
excites their resonant modes. In this work, we develop a model that bridges the mechanical …

The biological function and folding mechanisms of proteins are often guided by large-scale
slow motions, which involve crossing high energy barriers. In a simulation trajectory, these …

In this thesis, we propose a stimulus-responsive paradigm which integrates electromagnetic
(EM) and molecular communication (MC) by stimulating proteins in the human body. Our …

Proteins are not static structures; they must undergo conformational fluctuations about their
folded state to function. Typically, the slow, near-equilibrium conformational dynamics of …