This paper presents a molecular mechanics study using a molecular dynamics software (NAMD) coupled to virtual reality techniques for intuitive bio-nanorobotic prototyping. Using molecular dynamic simulations the operator can design, characterize and prototype the behavior of bio-nanorobotic components and structures. The main novelty of the proposed simulations is based on the characterization ...

Molecular motors play important roles within a biological cell, performing functions such as intracellular transport and gene transcription. Recent experimental work suggests that there are many plausible biochemical mechanisms that molecules such as myosin-V could use to achieve motion. To account for the abundance of possible discrete-stochastic frameworks that can arise when modeling molecul...

Molecular surfaces play an important role in studying the interactions between molecules. Visualizing the dynamic behavior of molecules is particularly interesting to gain insights into a molecular system. Only recently it has become possible to interactively visualize dynamic molecular surfaces using ray casting techniques. In this paper, we show how to further accelerate the construction and ...

Recent advances in atomic force microscopy, biomembrane force probe experiments, and optical tweezers allow one to measure the response of single molecules to mechanical stress with high precision. Such experiments, due to limited spatial resolution, typically access only one single force value in a continuous force profile that characterizes the molecular response along a reaction coordinate. ...

Molecular surface computations are often necessary in order to perform synthetic drug design A critical step in this process is the computation and update of an exact boundary representation for the molecular surface e g the Lee Richards sur face In this paper we introduce e cient techniques for computing a molecular sur face boundary representation as a set of NURBS non uniform rational B spli...

Dynamic behaviors of chemical concepts in density functional theory such as frontier orbitals (HOMO/LUMO), chemical potential, hardness, and electrophilicity index have been investigated in this work in the context of Bohn-Oppenheimer quantum molecular dynamics in association with molecular conformation changes. Exemplary molecular systems like CH5 , Cl (H2O)30 and Ca 2+ (H2O)15 are studied at ...

Abundant molecular oxygen was discovered in the coma of comet 67P/Churyumov-Gerasimenko. Its origin was ascribed to primordial gaseous O2 incorporated into the nucleus during the comet's formation. This thesis was put forward after discounting several O2 production mechanisms in comets, including photolysis and radiolysis of water, solar wind-surface interactions and gas-phase collisions. Here ...

We study self-replicating molecules under externally varying conditions. Changing conditions such as temperature variations and/or alterations in the environment’s resource composition lead to both non-constant replication and decay rates of the molecules. In general, therefore, molecular evolution takes place in a dynamic rather than a static fitness landscape. We incorporate dynamic replicati...

With the recent advancements in distributed computing, it is now possible to simulate molecular dynamics of large systems over unprecedented time scales. However, due to the sheer size of the generated trajectories, it is no longer possible to reliably extract relevant chemical and biological information from a simulation through visual inspection alone a single trajectory alone may consist of ...

Quasielastic neutron scattering measurements and molecular dynamics simulations were combined to investigate the collective dynamics of deuterated methanol, CD3OD. In the experimentally determined dynamic structure factor, a slow, non-Fickian mode was observed in addition to the standard density-fluctuation heat mode. The simulation results indicate that the slow dynamical process originates fr...