Molecular Dynamics Simulation

Epigenetic mechanism mediating the impact of child adversity on life-long adverse behavior

by Andrés Ginestet

Although epidemiological data provide evidence that early life experience plays a critical role in human development,... more Although epidemiological data provide evidence that early life experience plays a critical role in human development, the mechanism of how this works remains in question. Recent data from human and animal literature suggest that epigenetic changes, such as DNA methylation, are involved not only in cellular differentiation, but also in the modulation of genome function in response to early life experience affecting gene
function and the phenotype. Such modulations may serve as a mechanism for life-long genome adaptation.
These changes seem to be widely distributed across the genome and to involve central and peripheral systems. Examining the environmental circumstances associated with the onset and reversal of DNA methylation will be critical for understanding risk and resiliency.

Thermal Rectification in a Fluid Reservoir

by Ishwar Puri

Computational design of disulfide cyclic peptide as potential inhibitor of complex NS2B-NS3 dengue virus protease

by Arli Parikesit

Co-authored with Prof Usman Sumo Friend Tambunan, Nissia Apriyanti, William Chua and Katarina Wuryani

Development of genomic and proteomic studies coupled with computational sciences could facilitate the discovery of... more Development of genomic and proteomic studies coupled with computational sciences could facilitate the discovery of various target proteins and potential inhibitor to be developed as drugs. Several researches by molecular docking method have been conducted to design disulfide cyclic peptide ligand as potential inhibitors for NS2B-NS3 protease (NS2B-NS3 pro) of dengue virus serotype DENV-2 in order to inhibit replication of dengue virus. This research studied and evaluated the interaction of ligands and the enzyme in the hydrate state using molecular dynamics simulations at two different temperatures. Simulations were performed using two disulfide cyclic peptide inhibitors KRK and RKR, along with one linear peptide Bz-Nle-K-R-R-H as standard ligand. The result shows that dynamic movement of three proposed ligand in hydrated state affects ligand interactions. RKR ligand has the best affinity with the enzyme than KRK and standard ligand. This is shown by the ligand interaction with enzyme active site which remains stable during the simulation. At the end of simulation 300 K, RKR formed a hydrogen bond with Asp75 and at the end of simulation 312 K, RKR also maintained hydrogen bond with Asp75

Phylogeny and Phylogeography of insect bat Myotis muricola. 2012

by M.T. Abdullah, PhD

http://scholar.google.com.my/citations?hl=en&user=ylnvJSAAAAAJ

Myotis muricola is a widespread species covering the Malay Archipelago through the West and East of Wallace’s Line.... more Myotis muricola is a widespread species covering the Malay Archipelago through the West and East of Wallace’s Line. The genetic analysis, based on partial cytochrome b gene, shows the high genetic variation within M. muricola. The phylogenetic analysis has indicated that M. muricola in the Malay Archipelago are monophyletic. Members of M. muricola Eastern are grouped together independently of M. muricola Western and both groups are distantly related. On the other hand, M. muricola Western and M. muricola Eastern are distinct species and sister taxa to M. mystacinus. Based on the high genetic distance (26.8% to 38.5%) and the Genetic Species Concept (Baker & Bradley, 2006), it can be concluded that M. muricola Western and M. muricola Eastern should be considered as two distinct species. Furthermore, two subgroups within M. muricola Western, namely Sumatra-Asian and Bornean subgroups, are recognised as distinct subspecies (with genetic distance of 5.1% to 10.8%). The evidence from the molecular data indicated M. muricola Eastern as the ancestor of M. muricola species complex in the Malay Archipelago, which had earlier diverged into the western region during the Pliocene. Meanwhile, the geographical conditions during the Pleistocene had given more chances for fauna to diversify. It was predicted that M. muricola diverged in the western part of the Malay Archipelago during the Pleistocene when the sea level dropped and produced some landbridges among the islands in Sundaland. The hypothetical dispersal routes of M. muricola are related to the ancient Sunda River systems that produced gallery forest corridors for migration and which served as Pleistocene
refuges during the migration.

Phylogeny and Phylogeography of insect bat Myotis muricola (Gray, 1846) (Chiroptera: Vespertilionidae) from the West and and East of Wallace's Line Inferred from Partial MtDNA Cytochrome b Gene. Sigit Wiantoro, Ibnu Maryanto and M.T. Abdullah. 2012. Pertanika Journal of Tropical Agricultural Science 35(2): 271-292.

Analytical Bond-Order Potential for the Cadmium Telluride Binary System

by Bryan Wong

Physical Review B, 85, 115206 (2012)

Dynamics of a globular protein and its hydration water studied by neutron scattering and MD simulations

by Marco Lagi

Observation of high-temperature dynamic crossover in protein hydration water and its relation to reversible denaturation of lysozyme

by Marco Lagi

Logarithmic decay in single-particle relaxation of hydrated lysozyme powder

by Marco Lagi

Dynamic susceptibility of supercooled water and its relation to the dynamic crossover phenomenon

by Marco Lagi

The low-temperature dynamic crossover phenomenon in protein hydration water: simulations vs experiments

by Marco Lagi

Polarizable force fields and polarizable continuum model: a Fluctuating Charges/PCM approach. I: Theory and implementation

by Filippo Lipparini

Vibration and symmetry-breaking of boron-nitride nanotubes

by Rajib Chowdhury

Nanotechnology, 2010

The unique features of axial, torsional, transverse and radial breathing vibrations are captured for armchair and... more The unique features of axial, torsional, transverse and radial breathing vibrations are captured for armchair and zigzag singlewalled boron nitride nanotubes (BNNTs) based on molecular mechanics simulations and continuum mechanics theories. Equivalent Young's modulus 1TPa and shear modulus 0.4TPa are obtained independent of the chirality of BNNTs. In particular, a distorted optimized structure is observed for the first time for BNNTs with sufficiently large diameter and length. It is found that the deformed structures result in the behaviours of BNNTs deviating from those of classical columns/beams. Such symmetry breaking could also exert significant impacts on the structural instability (buckling) and the electronic properties of BNNTs that are sensitive to the structural symmetry.

The calibration of carbon nanotube based bio-nano sensors

by Rajib Chowdhury

Journal of Applied Physics, 107[12] (2010), pp. 124322:1-8.

We derive the calibration constants necessary for using single-walled carbon nanotubes (SWCNTs) as nano-scale mass... more We derive the calibration constants necessary for using single-walled carbon nanotubes (SWCNTs) as nano-scale mass sensors. The carbon nanotube resonators are assumed to be either in cantilevered or in bridged configurations. Two cases, namely when the added mass can be considered as a point mass and when the added mass is distributed over a larger area are considered. Closed-form transcendental equations have been derived for the frequency shift due to the added mass. Using the energy principles, generalized nondimensional calibration constants have been derived for an explicit relationship between the added mass and the frequency shift. A molecular mechanics model based on the universal force field potential is used to validate the new results presented. The results indicate that the distributed nature of the mass to be detected has considerable effect on the performance of the sensor.

Zeptogram sensing from gigahertz vibration: Graphene based nanosensor

by Rajib Chowdhury

Physica E: Low-dimensional Systems and Nanostructures

We develop the mathematical framework for using single layer graphene sheet as nanoscale label-free mass sensors.... more We develop the mathematical framework for using single layer graphene sheet as nanoscale label-free mass sensors. Graphene resonators are assumed to be in the cantilevered configuration. Four types of mass loadings are considered and closed-form equations are derived for the frequency shift due to the added mass. Using the potential and kinetic energy of the mass loaded graphene sheets, generalised non-dimensional calibration constants are proposed for an explicit relationship between the added mass and the frequency shift. These equations in turn are used for sensing the added mass. Numerical results illustrate that the sensitivity of graphene sensors is in the order of gigahertz/zeptogram. We show that the performance of the sensor depends on the spatial distribution of the attached mass on the graphene sheet.

Computational Improvements to Quantum Wave Packet ab Initio Molecular Dynamics Using a Potential-Adapted, Time-Dependent Deterministic Sampling Technique

by Isaiah Sumner

Proton Transport Pathways in [NiFe]-Hydrogenase

by Isaiah Sumner

Quantum wavepacket ab initio molecular dynamics: An approach for computing dynamically averaged vibrational spectra including critical nuclear quantum effects

by Isaiah Sumner

An Embedded-Atom Method Interatomic Potential for Pd-H Alloys

by Bryan Wong

Journal of Materials Research, 23, 704 (2008)

Accuracy of Existing Atomic Potentials for the CdTe Semiconductor Compound

by Bryan Wong

Journal of Chemical Physics, 134, 244703 (2011)

A Long-Range Electric Field Solver for Molecular Dynamics Based on Atomistic-to-Continuum Modeling

by Bryan Wong

Journal of Chemical Theory and Computation, 7, 1736 (2011)