TY - JOUR
T1 - Simulations of impulsive laser scattering of biological protein assemblies
T2 - Application to M13 bacteriophage
AU - Dykeman, Eric C.
AU - Benson, Daryn
AU - Tsen, Kong-Thon
AU - Sankey, Otto F.
PY - 2009/10/7
Y1 - 2009/10/7
N2 - We develop a theoretical framework, based on a bond-polarizability model, for simulating the impulsive force experienced on a protein or an assembly of proteins from a pulsed light source by coupling the laser electric field to an atomic distortion. The mechanism is impulsive stimulated Raman scattering (ISRS) where mechanical distortions produce variation in the electronic polarization through atomic displacements similar to vibrational Raman scattering. The magnitude of the impulsive force is determined from the empirical two-body bond-polarizability model and the intensity of the incident light. We apply the method to the M13 bacteriophage protein capsid system by performing several classical molecular-dynamics simulations that include the additional impulsive laser scattering force at various light intensities and pulse widths. The results of the molecular-dynamics simulations are then qualitatively interpreted with a simple harmonic oscillator model driven by ISRS. The intensity of light required to produce damage to the capsid in the simulations was found to be far higher than what was found in recent pulsed laser scattering experiments of M13 phage, suggesting that the observed inactivation of viruses with ultrashort laser pulses involves processes and/or mechanisms not taken into account in the present simulations.
AB - We develop a theoretical framework, based on a bond-polarizability model, for simulating the impulsive force experienced on a protein or an assembly of proteins from a pulsed light source by coupling the laser electric field to an atomic distortion. The mechanism is impulsive stimulated Raman scattering (ISRS) where mechanical distortions produce variation in the electronic polarization through atomic displacements similar to vibrational Raman scattering. The magnitude of the impulsive force is determined from the empirical two-body bond-polarizability model and the intensity of the incident light. We apply the method to the M13 bacteriophage protein capsid system by performing several classical molecular-dynamics simulations that include the additional impulsive laser scattering force at various light intensities and pulse widths. The results of the molecular-dynamics simulations are then qualitatively interpreted with a simple harmonic oscillator model driven by ISRS. The intensity of light required to produce damage to the capsid in the simulations was found to be far higher than what was found in recent pulsed laser scattering experiments of M13 phage, suggesting that the observed inactivation of viruses with ultrashort laser pulses involves processes and/or mechanisms not taken into account in the present simulations.
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U2 - 10.1103/PhysRevE.80.041909
DO - 10.1103/PhysRevE.80.041909
M3 - Article
C2 - 19905344
AN - SCOPUS:70350214571
SN - 1539-3755
VL - 80
JO - Physical Review E - Statistical, Nonlinear, and Soft Matter Physics
JF - Physical Review E - Statistical, Nonlinear, and Soft Matter Physics
IS - 4
M1 - 041909
ER -