Various aspects of the ab initio-based parametrization of an exciton model of amide I vibrations in peptides are discussed. Adopting "glycine dipeptide" (Ac-Gly-NHCH3) as a simple building-block model that describes the vibrational interaction between two peptide units, we perform comprehensive quantum-chemical calculations to investigate the effect and importance of the level of theory, the choice of local coordinates, and the localization method. A solvent continuum model description turns out important to obtain planar CONH peptide units when a full geometry optimization (which is necessary to obtain the correct frequencies) is performed. To study the conformational dependence of the amide I vibrations, we calculate (phi,psi) maps of the local-mode frequencies and couplings. Performing conformational averages of the (phi,psi) maps with respect to the most important peptide conformational states in solution (alpha, beta, P(II), and C5), we discuss the relation between these measurable quantities and the corresponding conformation of the peptide. Finally, the transferability of these maps to dipeptides with hydrophilic and hydrophobic side chains as well as to tripeptides with charged end groups is investigated.

A quantum-classical description of the amide I vibrational spectrum of trialanine cation in D2O is given that combines (i) a classical molecular dynamics simulation of the conformational distribution of the system, (ii) comprehensive density functional theory calculations of the conformation-dependent and solvent-induced frequency fluctuations, and (iii) a semiclassical description of the vibrational line shapes which includes nonadiabatic transitions between vibrational eigenstates. Various assumptions that are usually employed in the calculation of condensed-phase vibrational spectra are tested, including the adiabatic, the Franck-Condon, and the second-order cumulant approximations, respectively. All three parts of the theoretical formulation are shown to have a significant impact on the simulated spectrum, suggesting that the interpretation of peptide amide I spectra may require substantial theoretical support.

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Employing nonequilibrium molecular dynamics simulations, a comprehensive computational study of the photoinduced conformational dynamics of a photoswitchable bicyclic azobenzene octapeptide is presented. The calculation of time-dependent probability distributions along various global and local reaction coordinates reveals that the conformational rearrangement of the peptide is rather complex and occurs on at least four timescales: 1) After photoexcitation, the azobenzene unit of the molecule undergoes nonadiabatic photoisomerization within 0.2 ps. 2) On the picosecond timescale, the cooling (13 ps) and the stretching (14 ps) of the photoexcited peptide is observed. 3) Most reaction coordinates exhibit a 50-100 ps component reflecting a fast conformational rearrangement. 4) The 500-1000 ps component observed in the simulation accounts for the slow diffusion-controlled conformational equilibration of the system. The simulation of the photoinduced molecular processes is in remarkable agreement with time-resolved optical and infrared experiments, although the calculated cooling as well as the initial conformational rearrangements of the peptide appear to be somewhat too slow. Based on an ab initio parameterized vibrational Hamiltonian, the time-dependent amide I frequency shift is calculated. Both intramolecular and solvent-induced contributions to the frequency shift were found to change by < or = 2 cm(-1), in reasonable agreement with experiment. The potential of transient infrared spectra to characterize the conformational dynamics of peptides is discussed in some detail.

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This paper proposes a method for interpretation of the emotions detected in facial expressions in the context of the events that cause them. The method was developed to analyze the video recordings of facial expressions depicted during a collaborative game played as a part of the Mars-500 experiment. In this experiment, six astronauts were isolated for 520 days in a space station to simulate a flight to Mars. Seven time-dependent components of facial expressions were extracted from the video recordings of the experiment. To interpret these dynamic components, we proposed a mathematical model of emotional events. Genetic programming was used to find the locations, types, and intensities of the emotional events as well as the way the recorded facial expressions represented reactions to them. By classification of different statistical properties of the data, we found that there are significant relations between the facial expressions of different crew members and a memory effect between the collective emotional states of the crew members. The model of emotional events was validated on previously unseen video recordings of the astronauts. We demonstrated that both genetic search and optimization of the parameters improve the accuracy of the proposed model. This method is a step toward automating the analysis of affective expressions in terms of the cognitive appraisal theory of emotion, which relies on the dependence of the expressed emotion on the causing event.Index Terms-Appraisal theory of emotion, interpretation of affective expressions, Mars-500, mathematical modeling of affective interactions, second-person perspective.

Abstract. This paper presents a method for monitoring mental state of small isolated crews during long-term missions (such as space mission, polar expeditions, submarine crews, meteorological stations, and etc). It combines the records of negotiation game with monitoring of the nonverbal behavior of the players. We analyze the records of negotiation game that has taken place between the crew members who were placed in isolated environment for 105 days during the Mars-500 experiment. The outcomes of the analysis, differently from the previously made conclusions, show that there was not a significant deviation of the rational choice of the players. We propose an extension of the method that includes monitoring of the nonverbal behavior of the players next to recording the game records. The method is focused on those aspects of psychological and sociological states that are crucial for the performance of the crew. In particular, we focus on measuring of emotional stress, initial signs of conflicts, trust, and ability to collaborate.

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