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1.
J Nanosci Nanotechnol ; 14(2): 1549-62, 2014 Feb.
Article in English | MEDLINE | ID: mdl-24749441

ABSTRACT

The interaction of materials with ultrafast and ultraintense laser pulses is a current frontier of science both experimentally and theoretically. In this review, we briefly discuss some recent theoretical studies by the present authors with our method of semiclassical electron-radiation-ion dynamics (SERID). In particular, Zhou et al. and Jiang et al. respectively, determined the optimal duration and optimal timing for a series of femtosecond scale laser pulses to excite a specific vibrational mode in a general chemical system. A set of such modes can be used as a "fingerprint" for characterizing a particular molecule or a complex in a solid. One can therefore envision many applications, ranging from fundamental studies to detection of chemical or biological agents. Allen et al. proved that dimers are preferentially emitted during photofragmentation of C60 under an ultrafast and ultraintense laser pulse. For interactions between laser pulses and semiconductors, e.g., GaAs, Si and InSb, besides experimentally accessible optical properties--epsilon(omega) and chi(2)-Allen et al. offered many other indicators to confirm the nonthermal nature of structural changes driven by electronic excitations and occurring during the first few hundred femtoseconds. Lin et al. found that, after the application of a femtosecond laser pulse, excited electrons in materials automatically equilibrate to a Fermi-Dirac distribution within roughly 100 fs, solely because of their coupling to the nuclear motion, even though the resulting electronic temperature is one to two orders of magnitude higher than the kinetic temperature defined by the nuclear motion.


Subject(s)
Lasers , Models, Chemical , Models, Molecular , Nanostructures/chemistry , Nanostructures/ultrastructure , Computer Simulation , Macromolecular Substances/chemistry , Macromolecular Substances/radiation effects , Materials Testing , Molecular Conformation/radiation effects , Nanostructures/radiation effects , Particle Size , Surface Properties/radiation effects
2.
Theor Biol Med Model ; 10: 45, 2013 Jul 13.
Article in English | MEDLINE | ID: mdl-23849268

ABSTRACT

BACKGROUND: The most common bariatric surgery, Roux-en-Y gastric bypass, leads to glycemia normalization in most patients long before there is any appreciable weight loss. This effect is too large to be attributed purely to caloric restriction, so a number of other mechanisms have been proposed. The most popular hypothesis is enhanced production of an incretin, active glucagon-like peptide-1 (GLP-1), in the lower intestine. We therefore set out to test this hypothesis with a model which is simple enough to be robust and credible. METHOD: Our method involves (1) setting up a set of time-dependent equations for the concentrations of the most relevant species, (2) considering an "adiabatic" (or quasi-equilibrium) state in which the concentrations are slowly varying compared to reaction rates (and which in the present case is a postprandial state), and (3) solving for the dependent concentrations (of e.g. insulin and glucose) as an independent concentration (of e.g. GLP-1) is varied. RESULTS: Even in the most favorable scenario, with maximal values for (i) the increase in active GLP-1 concentration and (ii) the effect of GLP-1 on insulin production, enhancement of GLP-1 alone cannot account for the observations. I.e., the largest possible decrease in glucose predicted by the model is smaller than reported decreases, and the model predicts no decrease whatsoever in glucose ×insulin, in contrast to large observed decreases in homeostatic model assessment insulin resistance (HOMA-IR). On the other hand, both effects can be accounted for if the surgery leads to a substantial increase in some substance that opens an alternative insulin-independent pathway for glucose transport into muscle cells, which perhaps uses the same intracellular pool of GLUT-4 that is employed in an established insulin-independent pathway stimulated by muscle contraction during exercise. CONCLUSIONS: Glycemia normalization following Roux-en-Y gastric bypass is undoubtedly caused by a variety of mechanisms, which may include caloric restriction, enhanced GLP-1, and perhaps others proposed in earlier papers on this subject. However, the present results suggest that another possible mechanism should be added to the list of candidates: enhanced production in the lower intestine of a substance which opens an alternative insulin-independent pathway for glucose transport.


Subject(s)
Diabetes Mellitus, Type 2/surgery , Gastric Bypass , Blood Glucose/analysis , Diabetes Mellitus, Type 2/blood , Diabetes Mellitus, Type 2/physiopathology , Humans , Insulin/blood
3.
J Phys Chem A ; 115(3): 244-9, 2011 Jan 27.
Article in English | MEDLINE | ID: mdl-21166403

ABSTRACT

Using density-functional-based molecular dynamics simulations, we have performed comparative studies of the trans-cis isomerizations of azobenzene and bridged azobenzene (B-Ab) 5,6-dihydrodibenzo[c,g][1,2]diazocine induced by nπ* electronic excitation. The quantum yields found in our calculations, 45% for the bridged azobenzene versus 25% for azobenzene, are consistent with the experiment. Both isomerization processes involve two steps: (1) Starting from the trans structure, each molecule moves on its S(1) excited-state potential energy surface, via rotation around the NN bond, to an avoided crossing near the S(1)/S(0) conical intersection, where de-excitation occurs. (2) Subsequently, in the electronic ground state, there is further rotation around the NN bond, accompanied by twisting of the phenyl rings around their CN bonds, until the cis geometry is achieved. Because of its lower symmetry and smaller initial CNNC dihedral angle, the bridged azobenzene has a much shorter lifetime for the S(1) excited state, about 30 fs, as compared to about 400 fs for azobenzene. However, we find that the complete isomerizations have approximately the same time scales. Although the bridging feature in trans-B-Ab does not hinder rotation around the NN bond in step 1, it makes twisting of the two phenyl rings around the CN bonds much slower in step 2.

4.
J Phys Condens Matter ; 21(48): 485503, 2009 Dec 02.
Article in English | MEDLINE | ID: mdl-21832522

ABSTRACT

In our density-functional-based simulations of materials responding to femtosecond-scale laser pulses, we have observed a potentially useful phenomenon: the excited electrons automatically equilibrate to a Fermi-Dirac distribution within ∼100 fs, solely because of their coupling to the nuclear motion, even though the resulting electronic temperature is one to two orders of magnitude higher than the kinetic temperature defined by the nuclear motion. Microscopic simulations like these can then provide the separate electronic and kinetic temperatures, chemical potentials, pressures, and nonhydrostatic stresses as input for studies on larger lengths and timescales.

5.
J Phys Chem A ; 112(44): 11142-52, 2008 Nov 06.
Article in English | MEDLINE | ID: mdl-18847249

ABSTRACT

When a molecule is subjected to a short intense laser pulse, the ensuing dynamical processes depend qualitatively on the pulse parameters, including duration, frequency, and fluence. Here we report studies of cis to trans photoisomerization of azobenzene following femtosecond-scale laser pulses which are relatively short (10 fs) or long (100 fs) and which have a central frequency matched to either the first excited state (S1, or HOMO to LUMO in a molecular orbital picture) or the second (S2, or HOMO-1 to LUMO). The results presented here demonstrate that photoisomerization involves a rather intricate sequence of connected steps, with the nuclear and electronic degrees of freedom inextricably coupled. One important feature is the de-excitation required for the molecule to achieve its new ground-state after isomerization. If the primary excitation is to S1, then we find that only a single HOMO/LUMO avoided crossing is required and that this crossing occurs halfway along a rotational pathway involving the central CNNC dihedral angle. If the primary excitation is to S2, then the same HOMO/LUMO avoided crossing is observed, but it must be preceded by another avoided crossing that permits transfer of holes from the HOMO-1 to the HOMO, so that the HOMO is then able to accept electrons from the LUMO. We find that this earlier crossing can occur in either of two geometries, one near the cis configuration and the other near the trans. The fact that S2 (pi pi*) isomerization requires two steps may be related to the fact that isomerization yields are smaller for this (UV) excitation than for the S1 (n pi*, visible-light) excitation.

6.
J Chem Phys ; 126(2): 024502, 2007 Jan 14.
Article in English | MEDLINE | ID: mdl-17228958

ABSTRACT

Using semiclassical electron-radiation-ion dynamics, the authors have examined the effect of nuclear motion, resulting from both finite temperature and the response to a radiation field, on the line broadening of the excitation profile of 2,6-pyridinedicarboxylic acid (dipicolinic acid). With nuclei fixed, there is a relatively small broadening associated with the finite time duration of an applied laser pulse. When the nuclei are allowed to move, the excitation spectrum exhibits a much larger broadening, and is also reduced in height and shifted toward lower frequencies. In both cases, the excitation is due to well-defined pi to pi* transitions. The further inclusion of thermal motion at room temperature broadens the linewidth considerably because of variations in the molecular geometry: Transitions that had zero or negligible transition probabilities in the ground state geometry are weakly excited at room temperature.


Subject(s)
Bacillus anthracis/chemistry , Bacillus anthracis/isolation & purification , Magnetic Resonance Spectroscopy/methods , Models, Chemical , Models, Molecular , Picolinic Acids/analysis , Picolinic Acids/chemistry , Algorithms , Computer Simulation , Spores, Bacterial/chemistry , Spores, Bacterial/isolation & purification
7.
J Phys Chem A ; 111(6): 1133-7, 2007 Feb 15.
Article in English | MEDLINE | ID: mdl-17253665

ABSTRACT

Semiclassical electron-radiation-ion dynamics simulations are reported for the photodissociation of cyclobutane into two molecules of ethylene. The results clearly show the formation of the tetramethylene intermediate diradical, with dissociation completed in approximately 400 fs. In addition, the potential energy surfaces of the electronic ground state and lowest excited-state were calculated at the complete-active-space self-consistent-field/multireference second-order perturbation theory (CASSCF/MRPT2) level with 6-31G* basis sets, along the reaction path determined by the dynamics simulations. There are well-defined energy minima and maxima in the intermediate state region. It is found that both C-C-C bond bending and rotation of the molecule (around the central C-C bond) have important roles in determining the features of the potential energy surfaces for the intermediate species. Finally, the simulations and potential energy surface calculations are applied together in a discussion of the full mechanism for cyclobutane photodissociation.


Subject(s)
Cyclobutanes/chemistry , Thermodynamics , Cyclobutanes/radiation effects , Electrons , Ethylenes/chemical synthesis , Ethylenes/chemistry , Ethylenes/radiation effects , Free Radicals/chemical synthesis , Free Radicals/chemistry , Free Radicals/radiation effects , Models, Molecular , Photochemistry , Quantum Theory , Time Factors
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