Molecular Dynamics (MD) is used in computational heat transfer to determine the thermal response of nanostructures. Finding basis in classical statistical mechanics, MD relates the thermal energy of the atom to its momentum by the equipartition theorem. Momenta of atoms in an ensemble are determined by solving Newton’s equations with inter-atomic forces derived from Lennard-Jones potentials. St...

Atomistic molecular dynamics (MD) simulations of druglike molecules embedded in lipid bilayers are of considerable interest as models for drug penetration and positioning in biological membranes. Here we analyze partitioning of coumarin in dioleoylphosphatidylcholine (DOPC) bilayer, based on both multiple, unbiased 3 μs MD simulations (total length) and free energy profiles along the bilayer no...

The study of biomolecular interactions between a drug and its biological target is of paramount importance for the design of novel bioactive compounds. In this paper, we report on the use of molecular dynamics (MD) simulations and machine learning to study the binding mechanism of a transition state analogue (DADMe-immucillin-H) to the purine nucleoside phosphorylase (PNP) enzyme. Microsecond-l...

The reaction pathways characterizing macromolecular systems of biological interest are associated with high free energy barriers. Resorting to the standard all-atom molecular dynamics (MD) to explore such critical regions may be inappropriate as the time needed to observe the relevant transitions can be remarkably long. In this paper, we present a new method called Extended Diffusion-Map-direct...

To enable large-scale atomistic simulations of material processes involving chemical reactions, we have designed linear-scaling molecular dynamics (MD) algorithms based on an embedded divide-and-conquer (EDC) framework: first principles-based fast reactive forcefield (F-ReaxFF) MD; and quantum-mechanical MD in the framework of the density functional theory (DFT) on adaptive multigrids. To map t...

Myoglobin is an important protein for the study of structure and dynamics. Three conformational substates have been identified for the carbonmonoxy form of myoglobin (MbCO). These are manifested as distinct peaks in the IR absorption spectrum of the CO stretching mode. Ultrafast 2D IR vibrational echo chemical exchange experiments are used to observed switching between two of these substates, A...

Constant-pressure MD simulations complement constant-volume MD simulations and naturally allow the study of systems where external pressure is a driving force for a structural transformation. These transformations take place in crystalline as well as amorphous systems. Besides studies of bulk systems there is also growing interest in simulations of finite systems, such as clusters and nanocryst...

High precision approximation of the intermolecular potential is necessary for molecular dynamics (MD) simulations of the physical properties of molecular nitrogen (N2). Recently, Quantum Mechanical (QM) high precision calculations (coupled-cluster singles-anddoubles with a perturbative triples corrections [CCSD(T)]) were used to determine N2 – N2 intermolecular interaction. Using these data, th...

The transmembrane (TM) domain of the M2 channel protein from influenza A is a homotetrameric bundle of alpha-helices and provides a model system for computational approaches to self-assembly of membrane proteins. Coarse-grained molecular dynamics (CG-MD) simulations have been used to explore partitioning into a membrane of M2 TM helices during bilayer self-assembly from lipids. CG-MD is also us...

NMR spectroscopy and molecular dynamics (MD) simulation analyses of the chiral molecular micelles poly-(sodium undecyl-(L,L)-leucine-valine) (poly-SULV) and poly-(sodium undecyl-(L,L)- valine-leucine) (poly-(SUVL)) are reported. Both molecular micelles are used as chiral selectors in electrokinetic chromatography and each consists of covalently linked surfactant chains with chiral dipeptide hea...