A MOLECULAR DYNAMICS STUDY OF NANOWIRE RESONATOR BIO-OBJECT DETECTION

2021 ◽  
Author(s):  
ROSA FALLAHPOUR ◽  
RODERICK MELNIK
Keyword(s):  
Molecular Dynamics ◽  
Human Immunodeficiency Virus ◽  
Object Detection ◽  
Silicon Nanowire ◽  
Md Simulations ◽  
Comprehensive Analysis ◽  
Immunodeficiency Virus ◽  
Insight Into

This paper presents a comprehensive analysis, carried out by the molecular dynamics (MD) simulations, of the vibrations of silicon nanowire (SiNW) resonators, having diverse applications including biological and medical fields. The chosen approach allows us to obtain a better understanding of the nanowire (NW) materials’ characteristics, providing a more detailed insight into the behavior of nanostructures, especially when the topic of interest is relevant to their dynamics, interatomic interactions, and atoms trajectories’ prediction. We first simulate a SiNW to study its frequency of vibrations using MD simulations. Then, we add a molecule of human immunodeficiency virus as an example to investigate the potential of the SiNW resonator for the detection of tiny bio-objects. The developed technique and its application to the detection of tiny objects, such as viruses, are discussed in the context of several key effects pertinent to the design of SiNW.

Nanomechanical and Friction Properties of Ultrathin Amorphous Carbon Films Studied by Molecular Dynamics Analysis

2010 ◽  
Author(s):  
N. Wang ◽  
K. Komvopoulos
Keyword(s):  
Molecular Dynamics ◽  
Amorphous Carbon ◽  
Md Simulations ◽  
Carbon Films ◽  
Magnetic Storage ◽  
Disk Drives ◽  
Magnetic Medium ◽  
High Density Magnetic Recording ◽  
Protective Overcoats ◽  
Insight Into

An ultrathin (<4 nm) film of amorphous carbon (a-C) is used in contemporary disk drives to protect the magnetic medium of the hard disk from corrosion and mechanical wear due to intermittent impact of the low-flying magnetic head. Because of increasing demands for much higher magnetic storage densities (i.e., >10 Tbits/in2), the a-C film thickness must be decreased to <2 nm. However, the tribological and mechanical properties of such thin a-C films are not well understood and, moreover, are extremely difficult to determine experimentally. The objective of this study was to obtain insight into the tribological behavior of ultrathin a-C films by performing molecular dynamics (MD) simulations. MD results of the hardness and friction properties of nanometer-thick a-C films are interpreted in terms of the ratio of tetrahedral-to-trigonal carbon atom hybridization. A critical thickness for the effective protection of the magnetic medium by the a-C film is estimated from MD results. The results of this study elucidate the nanomechanical and nanotribological properties of ultrathin a-C films used as protective overcoats in extremely-high-density magnetic recording.

scholarly journals Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein

2019 ◽  
Author(s):  
David C. Wych ◽  
James S. Fraser ◽  
David L. Mobley ◽  
Michael E. Wall
Keyword(s):  
Molecular Dynamics ◽  
Rigid Body ◽  
Diffraction Data ◽  
Md Simulations ◽  
X Ray Diffraction ◽  
X Ray ◽  
Atom Pairs ◽  
Collective Motions ◽  
Rigid Body Motions ◽  
Insight Into

AbstractTo gain insight into crystalline protein dynamics, we performed molecular-dynamics (MD) simulations of a periodic 2×2×2 supercell of staphylococcal nuclease. We used the resulting MD trajectories to simulate X-ray diffraction and to study collective motions. The agreement of simulated X-ray diffraction with the data is comparable to previous MD simulation studies. We studied collective motions by analyzing statistically the covariance of alpha-carbon position displacements. The covariance decreases exponentially with the distance between atoms, which is consistent with a liquid-like motions (LLM) model, in which the protein behaves like a soft material. To gain finer insight into the collective motions, we examined the covariance behavior within a protein molecule (intra-protein) and between different protein molecules (inter-protein). The inter-protein atom pairs, which dominate the overall statistics, exhibit LLM behavior; however, the intra-protein pairs exhibit behavior that is consistent with a superposition of LLM and rigid-body motions (RBM). Our results indicate that LLM behavior of global dynamics is present in MD simulations of a protein crystal. They also show that RBM behavior is detectable in the simulations but that it is subsumed by the LLM behavior. Finally the results provide clues about how correlated motions of atom pairs both within and across proteins might manifest in diffraction data. Overall our findings increase our understanding of the connection between molecular motions and diffraction data, and therefore advance efforts to extract information about functionally important motions from crystallography experiments.

scholarly journals Dynamic Wetting on Moving Surfaces: A Molecular Dynamics Study

2012 ◽  
Author(s):  
Konstantinos Ritos ◽  
Nishanth Dongari ◽  
Yonghao Zhang ◽  
Jason M. Reese
Keyword(s):  
Molecular Dynamics ◽  
Contact Angle ◽  
Capillary Number ◽  
Contact Angle Hysteresis ◽  
Hydrophobic Surface ◽  
Md Simulations ◽  
Dynamic Wetting ◽  
Water Contact ◽  
Liquid Flows ◽  
Insight Into

We report molecular dynamics (MD) simulations of the dynamic wetting of nanoscale droplets on moving surfaces. The dynamic water contact angle and contact angle hysteresis are measured as a function of capillary number on smooth silicon and graphite surfaces. The hydrogen bonding and density profile variations are also reported, and the width of the water depletion layer is evaluated for droplets on three different static surfaces: silicon, graphite and a fictitious super-hydrophobic surface. Our results show that molecular displacements at the contact line are mostly influenced by interactions with the solid surface, while the viscous dissipation effects induced through the movement of surfaces are found to be negligible, especially for hydrophobic surfaces. This finding is in contrast with the wetting dynamics of macroscale droplets, which show significant dependence on the capillary number. This study may yield new insight into surface-wettability characteristics of nano droplets, in particular, developing new boundary conditions for continuum solvers for liquid flows in micro- and nanoscale devices.

scholarly journals Intracellular Accumulation of Human Immunodeficiency Virus Protease Inhibitors

2002 ◽  
Vol 46 (10) ◽  
pp. 3228-3235 ◽  
Author(s):  
Saye H. Khoo ◽  
Patrick G. Hoggard ◽  
Ian Williams ◽  
E. Rhiannon Meaden ◽  
Philippa Newton ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Protease Inhibitors ◽  
Plasma Viral Load ◽  
Plasma Drug Concentration ◽  
Drug Penetration ◽  
Plasma Drug ◽  
Intracellular Accumulation ◽  
Human Immunodeficiency Virus Protease ◽  
Immunodeficiency Virus ◽  
Insight Into

ABSTRACT Intracellular accumulation of the protease inhibitors (PIs) saquinavir (SQV), ritonavir (RTV), and indinavir (IDV) was determined in 50 human immunodeficiency virus-positive patients. Following extraction, PIs were quantified by mass spectrometry. Paired plasma and intracellular samples were collected over a full dosing interval from patients (13 on SQV, 6 on RTV, 8 on IDV, 16 on SQV plus RTV, 7 on IDV plus RTV) with a plasma viral load of <400 copies/ml. Data were expressed as intracellular/plasma drug concentration ratios. A hierarchy of intracellular accumulation was demonstrated by the following medians: 9.45 for SQV > 1.00 for RTV > 0.51 for IDV. Coadministration of RTV did not boost ratios of SQV or IDV within the cell or in plasma, although absolute plasma and intracellular SQV concentrations were increased by RTV. Seven individuals receiving SQV in hard-gel capsule form (median, 32 months) had higher intracellular/plasma drug ratios than all other patients receiving SQV (median, 17.62 versus 4.83; P = 0.04), despite consistently low plasma SQV concentrations. How this occurs may provide insight into the mechanisms that limit adequate drug penetration into sanctuary sites.

scholarly journals Human immunodeficiency virus-negative plasmablastic lymphoma: A comprehensive analysis of 114 cases

2015 ◽  
Vol 33 (4) ◽  
pp. 1615-1620 ◽  
Author(s):  
MIN LIU ◽  
BAILONG LIU ◽  
BIN LIU ◽  
QIANG WANG ◽  
LIJUAN DING ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Comprehensive Analysis ◽  
Plasmablastic Lymphoma ◽  
Immunodeficiency Virus

THE STUDY OF HIV INFECTION IN CHINESE ANTIRETROVIRAL THERAPY PATIENTS

2014 ◽  
Vol 22 (01) ◽  
pp. 73-88
Author(s):  
JIE LOU ◽  
HONGMEI ZHANG ◽  
QUANBI ZHAO ◽  
LINGJIE LIAO ◽  
LITAO HAN
Keyword(s):  
Human Immunodeficiency Virus ◽  
T Cells ◽  
Hiv Infection ◽  
Cd4 T Cells ◽  
Mathematics Model ◽  
Highly Active ◽  
Immunodeficiency Virus ◽  
Memory Cd4 T Cells ◽  
Insight Into

Analysis of changes in viral load after initiation of treatment with potent antiretroviral agents has provided substantial insights into the dynamics of human immunodeficiency virus type 1. We built a simple mathematics model to study the effect of latent-infected resting memory CD4+ T cells during the HIV infection and highly active anti-retroviral therapy (HAART). Through analysis of eight patients who received HAART in China, we have an insight into the mechanisms of resting memory CD4+ T cells in HIV infection. Simulations show that new infections still exist in the eight patients even under the HAART. Also, because of the long half-life of resting infected memory CD4+ T cells, removal of HIV from patient could take considerably longer time or be unattainable.

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