One more reason why the Davydov soliton may be thermally stable

The thermal stability of the Davydov soliton is still an open problem. Recent studies have shown that the Davydov soliton may be stable at 300°C if the coupling constant of the amide-I excitons with the motion of the peptide groups is larger than that estimated from experimental data. However, the coupling constant cannot be changed artificially in the real situation. Here we show that it is possible to produce an additional nonlinear force for the self-trapping of the amide-I vibrational energy when taking account of the exciton-exciton interactions and this is equivalent to an increase of the coupling constant. This may provide a possible solution to the problem of the thermal stability of the Davydov soliton.     

The Features of Infrared Absorption of the Protein Molecules in the Living System

We utilize a vibron-soliton model for amide-I vibrational quanta interacting with optical phonons to study the feature of infrared absorption of the protein molecules with finite temperatuse.The self-trapping of amide-Ik vibrational quantum results in red shift of the main peak and largely anomalous band to occur in the infrared absorption for the protein molecules.utilizing the concise model of vibron and improved theory of color centers we have given theoretically the value of red shifts of the main peak and the intensity of anomalous band in infrared absorption,respectively,the latter reduces with increasing temperature which is consistent with the experimental result.     

多肽和蛋白质酰胺-I带振动频率图的温度依赖性

利用高温分子动力学模拟和红外光谱实验手段,研究了一个基于分子力学力场的酰胺-I带振动频率图的温度依赖性. 结果表明,基于298 K所建立的频率图可以应用上至500 K的分子动力学轨迹,所模拟的红外光谱能够很好地重复88 oC时的实验光谱. 另外还模拟了两个含有天然和非天然氨基酸残基的三肽分子的红外光谱,与实验结果相比得到了较好的符合. 结果表明,所建立的频率图能够用于获得多肽体系在不同温度下的酰胺-I带局域模振动频率及其分布,有助于深入认识多肽的热去折叠物种的红外光谱特征.     

Experimental and computational study of N-methylacetamide

We report on recent Raman experiments in liquid N-methylacetamide and compare with computational results using a nonlinear quantum mechanical model. In the 100 cm^-1 region there is qualitative agreement between experimental and computational results. In the amide-I region (about 1650 cm^-1) a new band appears at low temperatures, and it is suggested that this result can be explained in terms of self-trapped states, which occur in the present theoretical model.     

Temperature Effect of Infrared Rays Absorbed by the Protein Molecules in the Living Systems

The principal features of Infrared absorption of the protein molecules are anomalous red shifts of the main peaks and increases of intensity of the anomalous bands with decreasing temperature which are proved by experiments. We think that these anomalous phenomena are caused by the self-trapping of amide-I vibrational quantum (vibron). We thus proposed a soliton model of the vibrons interacting with optical vibration of amino acid residue (phonon) to study theoretically these phenomena. We find farther out the exponential-reductions of the intensity of the anomalous bands in the infrared absorption with increasing temperature in the protein molecules by using this model. This shows that the living things including human beings and animals can absorb more much infrared lights at low temperature than that at high temperature.     

胶原蛋白分子中电场激发的孤子特性

根据胶原蛋白分子的结构特点，建立了新的胶原蛋白分子模型，得到了更能体现胶原蛋白分 子三维结构的系统哈密顿量，并采用4阶Runge-Kutta算法，对得到的电场作用下胶原蛋白分 子中激发态能量传递的动力学方程进行了数值求解.结果表明电场脉冲可以在胶原蛋白分子 中激发起酰胺键(amide-Ⅰ)振子的孤波，且在孤子产生的同时伴随有声子发射. 关键词： 胶原蛋白 孤子 电场     

NONLINEARLY VIBRATIONAL ENERGY-SPECTRA OF MOLECULAR CRYSTALS

The nonlinear quantum vibrational energy spectra of amide-I in the molecular crystals acetanilide are calculated by using the discrete nonlinear Schr?dinger equation appropriate to this kind of crystals.The numerical results obtained by this method are in good agreement with the experimental values. Meanwhile, the energy levels at high excited states have also been obtained for the acetanilide, which is helpful in researching the Raman scattering and infrared absorption properties of the this kind of crystals.     

Theory of bio-energy transport in protein molecules and its experimental evidences as well as applications ( I )

A new theory of bio-energy transport along protein molecules, where energy is released by the hydrolysis of adenosine triphosphate (ATP), has recently been proposed for some physical and biological reasons. In this theory, Davydov’s Hamiltonian and wave function of the systems are simultaneously improved and extended. A new interaction has been added into the original Hamiltonian. The original wave function of the excitation state of single particles has been replaced by a new wave function of the two-quanta quasi-coherent state. In such a case, bio-energy is carried and transported by the new soliton along protein molecular chains. The soliton is formed through the self-trapping of two excitons interacting with amino acid residues. The exciton is generated by the vibration of amide-I (C=O stretching) arising from the energy of the hydrolysis of ATP. The properties of the soliton are extensively studied by analytical methods and its lifetime for a wide range of parameter values relevant to protein molecules is calculated using the nonlinear quantum perturbation theory. The lifetime of the new soliton at the biological temperature of 300 K is large enough and belongs to the order of 10^-10 s or τ/τ₀ ≥ 700. The different properties of the new soliton are further studied. The results show that the new soliton in the new model is a better carrier of bio-energy transport and it can play an important role in biological processes. This model is a candidate of the bio-energy transport mechanism in protein molecules.     

Theory of bio-energy transport in protein molecules and its experimental evidences as well as applications (I)

A new theory of bio-energy transport along protein molecules, where energy is released by the hydrolysis of adenosine triphosphate (ATP), has recently been proposed for some physical and biological reasons. In this theory, Davydov’s Hamiltonian and wave function of the systems are simultaneously improved and extended. A new interaction has been added into the original Hamiltonian. The original wave function of the excitation state of single particles has been replaced by a new wave function of the two-quanta quasi-coherent state. In such case, bio-energy is carried and transported by the new soliton along protein molecular chains. The soliton is formed through the self-trapping of two excitons interacting with amino acid residues. The exciton is generated by the vibration of amide-I (C=O stretching) arising from the energy of the hydrolysis of ATP. The properties of the soliton are extensively studied by analytical methods and its lifetime for a wide range of parameter values relevant to protein molecules is calculated using the nonlinear quantum perturbation theory. The life-time of the new soliton at the biological temperature of 300 K is large enough and belongs to the order of 10⁻¹⁰ s or τ/τ ₀ ⩾ 700. The different properties of the new soliton are further studied. The results show that the new soliton in the new model is a better carrier of bio-energy transport and it can play an important role in biological processes. This model is a candidate of the bio-energy transport mechanism in protein molecules.      

Nonrelativistic limit of Dirac-Fock codes: the role of Brillouin configurations

We solve a long standing problem with relativistic calculations done with the widely used multiconfiguration Dirac-Fock method. We show, using relativistic many-body perturbation theory (RMBPT), how, even for relatively high-Z, relaxation or correlation causes the nonrelativistic limit of states of different total angular momentum but identical orbital angular momentum to have different energies. We show that only large scale calculations that include all single excitations, even those obeying Brillouin's theorem, have the correct limit. We reproduce very accurately recent high-precision measurements in F-like Ar, and turn then to a precise test of QED. We obtain the correct nonrelativistic limit not only for fine structure but also for level energies and show that RMBPT calculations are not immune to this problem.     

Investigation of Galilean invariance of multi-phase lattice Boltzmann methods

We examine the Galilean invariance of standard lattice Boltzmann methods for two-phase fluids. We show that the known Galilean invariant term that is cubic in the velocities, and is usually neglected, is a major source of Galilean invariance violations. We show that incorporating a correction term can improve the Galilean invariance of the method by up to two orders of magnitude for large velocities. We found that this is true in particular for methods in which the interactions are incorporated through a forcing term. Methods in which interactions are incorporated through a non-ideal pressure tensor only benefit for large velocities.     

Different Hagedorn temperatures for mesons and baryons from experimental mass spectra

We analyze the light-flavor particle mass spectra and show that in the region up to 1.8 GeV the Hagedorn temperature for mesons is significantly larger than for baryons, reflecting the fact that the number of baryon states grows more rapidly with the mass. We show that in dual string models the ratio of the mesonic to baryonic Hagedorn temperatures is equal to .     

Controlling soliton explosions

We investigate the dynamics of solitons in generalized Klein–Gordon equations in the presence of nonlinear damping and spatiotemporal perturbations. We will present different mechanisms for soliton explosions. We show (both analytically and numerically) that some space-dependent perturbations or nonlinear damping can make the soliton internal mode unstable leading to soliton explosion. We will show that, in some cases, while some conditions are satisfied, the soliton explodes becoming a permanent, extremely complex, spatiotemporal dynamics. We believe these mechanisms can explain some of the phenomena that recently have been reported to occur in excitable media. We present a method for controlling soliton explosions.     

A generalization of the algebraic approach for effective interactions in nuclei

We generalize the algebraic approach of Schucan and Weidenmüller for effective interactions in nuclei and show that in general one obtains an effecti to that of Brandow by an arbitrary similarity transformation. We then show how this arbitrariness can be utilized to obtain hermitian effective interac     

Many fields interaction: Beam splitters and waveguide arrays

We study the interaction of many fields. We obtain an effective Hamiltonian for this system by using a method recently introduced that produces a small rotation to the Hamiltonian that allows to neglect some terms in the rotated Hamiltonian. We show that coherent states remain coherent under the action of a quadratic Hamiltonian and by solving the eigenvalue and eigenvector problem for tridiagonal matrices we also show that a system of n interacting harmonic oscillators, initially in coherent states, remain coherent during the interaction.     

Resummed corrections to the ρ parameter in the complex mass scheme

We present all order results for the heavy top corrections to the ρ parameter in the complex mass scheme. We derive translation formulas between the complex mass and the on-shell scheme and show that they are ultimately equivalent. We show that a naive treatment with a fixed width for the top quark cannot give even approximately correct results.     

Separability,gauge invariance and nonsuperluminality in direct interaction dynamics

We discuss the classical mechanics of relativistic systems with direct interaction. We show that various desiderata can all be accommodated in the single time approach by restricting the observables to the gauge invariant variables. We show how such observables can be constructed in general. We explicitly construct position observables in a general system and show that they lead to separable, invariant world lines. Nonsuperluminality is explicitly demonstrated for two body systems interacting via central forces of semibounded magnitude provided they ensure timelike canonical momenta. For two particles, our results reproduce the usual solution in covariant equal-time gauge.     

Floquet solutions for the 1-dimensional quasi-periodic Schrödinger equation

We show that the 1-dimensional Schrödinger equation with a quasiperiodic potential which is analytic on its hull admits a Floquet representation for almost every energyE in the upper part of the spectrum. We prove that the upper part of the spectrum is purely absolutely continuous and that, for a generic potential, it is a Cantor set. We also show that for a small potential these results extend to the whole spectrum.