How superlocalization affects Vibrational Energy Exchange process in proteins

Examining the origins of observed terahertz modes from an optically pumped atomistic model protein in aqueous solution

The microscopic origins of terahertz (THz) vibrational modes in biological systems are an active and open area of current research. Recent experiments [Physical Review X 8, 031061 (2018)] have revealed the presence of a pronounced mode at $\sim$0.3 THz in fluorophore-decorated bovine serum albumin (BSA) protein in aqueous solution under nonequilibrium conditions induced by optical pumping. This result was heuristically interpreted as a collective elastic fluctuation originating from the activation of a low-frequency phonon mode. In this work, we show that the sub-THz spectroscopic response eme…

Thermodynamic stability of small-world oscillator networks: A case study of proteins

We study vibrational thermodynamic stability of small-world oscillator networks, by relating the average mean-square displacement $S$ of oscillators to the eigenvalue spectrum of the Laplacian matrix of networks. We show that the cross-links suppress $S$ effectively and there exist two phases on the small-world networks: 1) an unstable phase: when $p\ll1/N$, $S\sim N$; 2) a stable phase: when $p\gg1/N$, $S\sim p^{-1}$, \emph{i.e.}, $S/N\sim E_{cr}^{-1}$. Here, $p$ is the parameter of small-world, $N$ is the number of oscillators, and $E_{cr}=pN$ is the number of cross-links. The results are ex…

蛋白质-水能传递 via 非谐低频振动

Protein-Water Energy Transfer via Anharmonic Low-Frequency Vibrations

本研究通过非谐低频振动分析，揭示了蛋白质将多余热能传递给溶剂的机制，发现远红外范围内的振动能量传输主导整体热传输。

The Glass-like Structure of Globular Proteins and the Boson Peak

Vibrational spectra of proteins and topologically disordered solids display a common anomaly at low frequencies, known as Boson peak. We show that such feature in globular proteins can be deciphered in terms of an energy landscape picture, as it is for glassy systems. Exploiting the tools of Euclidean random matrix theory, we clarify the physical origin of such anomaly in terms of a mechanical instability of the system. As a natural explanation, we argue that such instability is relevant for proteins in order for their molecular functions to be optimally rooted in their structures.

Topological phonon modes and their role in dynamic instability of microtubules

Microtubules (MTs) are self-assembled hollow protein tubes playing important functions in live cells. Their building block is a protein called tubulin, which self-assembles in a particulate 2 dimensional lattice. We study the vibrational modes of this lattice and find Dirac points in the phonon spectrum. We discuss a splitting of the Dirac points that leads to phonon bands with nonzero Chern numbers, signaling the existence of topological vibrational modes localized at MTs edges, which we indeed observe after explicit calculations. Since these modes are robust against the large changes occurri…

Vibrational structures and long-lasting electronic coherence

Recent observations of beating signals in the excitation energy transfer dynamics of photosynthetic complexes have been interpreted as evidence for sustained coherences that are sufficiently long-lived for energy transport and coherence to coexist. The possibility that coherence may be exploited in biological processes has opened up new avenues of exploration at the interface of physics and biology. The microscopic origin of these long-lived coherences, however, remains to be uncovered. Here we present such a mechanism and verify it by numerically exact simulations of system-environment dynami…

通过光泵浦激发大分子中的非平衡态

Exciting out-of-equilibrium states in macromolecules through light pumping

针对蛋白质吸收光后向内部振动模式的能量下转换问题，本文研究荧光团光激发如何将电子激发能量转移为声子激发，以解释声子凝聚的初始环节。

Elastic properties of proteins: insight on the folding process and evolutionary selection of native structures

We carry out a theoretical study of the vibrational and relaxation properties of naturally-occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model we provide a full characterization of the spectrum and eigenmodes of vibration at various temperatures by merely exploiting the knowledge of the protein native structure. It is shown that the rate at which perturbations decay at the folding transition correlates well with experimental folding rates. This validation is carried out on a list of about 30 two-state folders. Furt…