Search results for "molecular"
showing 10 items of 32340 documents
BioImageXD: an open, general-purpose and high-throughput image-processing platform
2012
BioImageXD puts open-source computer science tools for three-dimensional visualization and analysis into the hands of all researchers, through a user-friendly graphical interface tuned to the needs of biologists. BioImageXD has no restrictive licenses or undisclosed algorithms and enables publication of precise, reproducible and modifiable workflows. It allows simple construction of processing pipelines and should enable biologists to perform challenging analyses of complex processes. We demonstrate its performance in a study of integrin clustering in response to selected inhibitors.
Ultrafast electronic relaxation and vibrational cooling dynamics of Au 144(SC2H4Ph)60 nanocluster probed by transient mid-IR spectroscopy
2014
Energy relaxation dynamics of a gold nanocluster with atomically precise composition, Au144(SC2H4Ph)60, is studied by transient mid-IR spectroscopy. The experiment is designed to simultaneously pro...
TDDFT Analysis of Optical Properties of Thiol Monolayer-Protected Gold and Intermetallic Silver–Gold Au144(SR)60 and Au84Ag60(SR)60 Clusters
2014
The optical absorption spectra of atomistic model structures for experimentally isolated all-gold Au144(SR)60 and intermetallic Au84Ag60(SR)60 clusters are systematically analyzed from linear-response time-dependent density functional theory (LR-TDDFT) and time-dependent density functional perturbation theory (TD-DFPT) calculations. The computed spectra, utilizing the atomistic model for Au144(SR)60 published by us in 2009, reproduce closely the experimental observations for corresponding isolated compounds, reported previously by Kumara and Dass in 2011. A collective dipole oscillation within the metal cores of the all-gold and intermetallic clusters is formed as response to light in the v…
Vibrational Perturbations and Ligand–Layer Coupling in a Single Crystal of Au144(SC2H4Ph)60 Nanocluster
2015
We have determined vibrational signatures and optical gap of the Au144(PET)60 (PET: phenylethylthiol, SC2H4Ph) nanocluster solvated in deuterated dichloromethane (DCM-D2, CD2Cl2) and in a single crystal. For crystals, solid-state (13)C NMR and X-ray diffraction were also measured. A revised value of 2200 cm(-1) (0.27 eV) was obtained for the optical gap in both phases. The vibrational spectra of solvated AU144(PET)60 closely resembles that of neat PET, while the crystalline-state spectrum exhibits significant inhomogeneous spectral broadening, frequency shifts, intensity transfer between vibrational modes, and an increase in the overtone and combination transition intensities. Spectral broa…
Molecule-like photodynamics of Au102(pMBA)44 nanocluster.
2015
Photophysical properties of a water-soluble cluster Au102(pMBA)44 (pMBA = para-mercaptobenzoic acid) are studied by ultrafast time-resolved mid-IR spectroscopy and density functional theory calculations in order to distinguish between molecular and metallic behavior. In the mid-IR transient absorption studies, visible or near-infrared light is used to electronically excite the sample, and the subsequent relaxation is monitored by studying the transient absorption of a vibrational mode in the ligands. Based on these studies, a complete picture of energy relaxation dynamics is obtained: (1) 0.5-1.5 ps electronic relaxation, (2) 6.8 ps vibrational cooling, (3) intersystem crossing from the low…
Role of Vibrational Dynamics in Electronic Relaxation of Cr(acac)3
2015
Ultrafast energy relaxation of Cr(acac)3 dissolved in tetrachloroethylene (TCE) is studied by time-resolved infrared (TRIR) spectroscopy by using electronic and vibrational excitation. After electronic excitation at 400 or 345 nm, the ground state recovers in two time scales: 15 ps (major pathway) and 800 ps (minor pathway), corresponding to fast electronic transition to the ground state and intermediate trapping on the long-lived (2)E state followed by intersystem crossing (ISC) to the ground state. The quantum yield for the fast recovery of the ground state depends on the excitation wavelength, being higher for 345 nm. Vibrational cooling (VC) occurs on the electronic excited states with …
A Unified AMBER-Compatible Molecular Mechanics Force Field for Thiolate-Protected Gold Nanoclusters.
2016
We present transferable AMBER-compatible force field parameters for thiolate-protected gold nanoclusters. Five different sized clusters containing both organo-soluble and water-soluble thiolate ligands served as test systems in MD simulations, and parameters were validated against DFT and experimental results. The cluster geometries remain intact during the MD simulations in various solvents, and structural fluctuations and energetics showed agreement with DFT calculations. Experimental diffusion coefficients and crystal structures were also reproduced with sufficient accuracy. The presented parameter set contains the minimum number of cluster-specific parameters enabling the use of these p…
Symmetry breaking in ligand-protected gold clusters probed by nonlinear optics
2016
The first hyperpolarizabilities of [Au25(SR)18](-1/0) and Au38(SR)24 clusters were determined by Hyper-Rayleigh Scattering. A strong dependence on the molecular symmetry was observed, and we explore two strategies to destroy the center of inversion in [Au25(SR)18](-1/0), protection by chiral ligands and alloying of the cluster with silver. This may open new avenues to applications of Au : SR clusters in second-order nonlinear optics.
Force Distribution Analysis of Mechanochemically Reactive Dimethylcyclobutene
2013
Internal molecular forces can guide chemical reactions, yet are not straightforwardly accessible within a quantum mechanical description of the reacting molecules. Here, we present a force-matching force distribution analysis (FM-FDA) to analyze internal forces in molecules. We simulated the ring opening of trans-3,4-dimethylcyclobutene (tDCB) with on-the-fly semiempirical molecular dynamics. The self-consistent density functional tight binding (SCC-DFTB) method accurately described the force-dependent ring-opening kinetics of tDCB, showing quantitative agreement with both experimental and computational data at higher levels. Mechanical force was applied in two different ways, namely, exter…
Curvelet-based method for orientation estimation of particles from optical images
2014
A method based on the curvelet transform is introduced to estimate the orientation distribution from two-dimensional images of small anisotropic particles. Orientation of fibers in paper is considered as a particular application of the method. Theoretical aspects of the suitability of this method are discussed and its efficiency is demonstrated with simulated and real images of fibrous systems. Comparison is made with two traditionally used methods of orientation analysis, and the new curvelet-based method is shown to perform better than these tradi- tional methods. © The Authors. Published by SPIE under a Creative Commons Attribution 3.0 Unported License. Distribution or reproduction of th…