Browse
Submit Data
Databases
API
Help

Dataset Information

23 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Evaluating the role of coherent delocalized phonon-like modes in DNA cyclization.

ABSTRACT: The innate flexibility of a DNA sequence is quantified by the Jacobson-Stockmayer's J-factor, which measures the propensity for DNA loop formation. Recent studies of ultra-short DNA sequences revealed a discrepancy of up to six orders of magnitude between experimentally measured and theoretically predicted J-factors. These large differences suggest that, in addition to the elastic moduli of the double helix, other factors contribute to loop formation. Here, we develop a new theoretical model that explores how coherent delocalized phonon-like modes in DNA provide single-stranded "flexible hinges" to assist in loop formation. We combine the Czapla-Swigon-Olson structural model of DNA with our extended Peyrard-Bishop-Dauxois model and, without changing any of the parameters of the two models, apply this new computational framework to 86 experimentally characterized DNA sequences. Our results demonstrate that the new computational framework can predict J-factors within an order of magnitude of experimental measurements for most ultra-short DNA sequences, while continuing to accurately describe the J-factors of longer sequences. Further, we demonstrate that our computational framework can be used to describe the cyclization of DNA sequences that contain a base pair mismatch. Overall, our results support the conclusion that coherent delocalized phonon-like modes play an important role in DNA cyclization.

SUBMITTER: Alexandrov LB

PROVIDER: S-EPMC5575098 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Observation of coherent delocalized phonon-like modes in DNA under physiological conditions.

Project description:Underdamped terahertz-frequency delocalized phonon-like modes have long been suggested to play a role in the biological function of DNA. Such phonon modes involve the collective motion of many atoms and are prerequisite to understanding the molecular nature of macroscopic conformational changes and related biochemical phenomena. Initial predictions were based on simple theoretical models of DNA. However, such models do not take into account strong interactions with the surrounding water, which is likely to cause phonon modes to be heavily damped and localized. Here we apply state-of-the-art femtosecond optical Kerr effect spectroscopy, which is currently the only technique capable of taking low-frequency (GHz to THz) vibrational spectra in solution. We are able to demonstrate that phonon modes involving the hydrogen bond network between the strands exist in DNA at physiologically relevant conditions. In addition, the dynamics of the solvating water molecules is slowed down by about a factor of 20 compared with the bulk.

| S-EPMC4895446 | biostudies-literature

Nanoscale coherent phonon spectroscopy.

Project description:Coherent phonon spectroscopy can provide microscopic insight into ultrafast lattice dynamics and its coupling to other degrees of freedom under nonequilibrium conditions. Ultrafast optical spectroscopy is a well-established method to study coherent phonons, but the diffraction limit has hampered observing their local dynamics directly. Here, we demonstrate nanoscale coherent phonon spectroscopy using ultrafast laser-induced scanning tunneling microscopy in a plasmonic junction. Coherent phonons are locally excited in ultrathin zinc oxide films by the tightly confined plasmonic field and are probed via the photoinduced tunneling current through an electronic resonance of the zinc oxide film. Concurrently performed tip-enhanced Raman spectroscopy allows us to identify the involved phonon modes. In contrast to the Raman spectra, the phonon dynamics observed in coherent phonon spectroscopy exhibit strong nanoscale spatial variations that are correlated with the distribution of the electronic local density of states resolved by scanning tunneling spectroscopy.

| S-EPMC9586471 | biostudies-literature

Morphology-Dependent Coherent Acoustic Phonon Vibrations and Phonon Beat of Au Nanopolyhedrons.

Project description:Coherent acoustic phonon vibrations of Au nanopolyhedrons, including nanocubes, nano-octahedrons, and nanocuboctahedrons, in aqueous solutions and poly(vinyl alcohol) (PVA) films, were investigated using transient absorption (TA) spectroscopy combined with finite element analysis based on continuum elastic theory. In each type of nanopolyhedron, two vibrational modes with similar quality factors (Qs) and phases were observed, suggesting that both were induced by thermal expansion. The low-frequency vibrational mode represents a tip-to-tip displacement in each nanopolyhedron, whereas the high-frequency mode is the breathing vibration of the whole particle and reveals morphology dependence, displaying a face-to-face displacement in nanocuboctahedrons, an edge-to-edge displacement in nano-octahedrons, and a combination of face-to-face and edge-to-edge displacements in nanocubes. Moreover, a clear phonon beat was identified in the two vibrational modes of the nanocuboctahedrons. Our experimental results provide a possible application of morphology-controllable metal nanoresonators.

| S-EPMC7931377 | biostudies-literature

An Analog of electrically induced transparency via surface delocalized modes.

Project description:We demonstrate theoretically and experimentally an interesting opaque state, which is based on an analog of electromagnetically induced transparency (EIT) in mechanism, in a metal hole array of the dimer lattice. By introducing a small difference to the dimer holes of each unit cell, the surface delocalized modes launching out from the dimer holes can have destructive interferences. Consequently, a narrow opaque window in the transparent background can be observed in the transmission spectrum. This surface-mode-induced opacity (SMIO) state is very sensitive to the difference of the dimer holes, which will promise various applications.

| S-EPMC4508561 | biostudies-literature

Electron-phonon coupling in topological surface states: The role of polar optical modes.

Project description:The use of topological edge states for spintronic applications could be severely hampered by limited lifetimes due to intrinsic many-body interactions, in particular electron-phonon coupling. Previous works to determine the intrinsic coupling strength did not provide a coherent answer. Here, the electron-phonon interaction in the metallic surface state of 3D topological insulators is revised within a first principles framework. For the archetypical cases of Bi2Se3 and Bi2Te3, we find an overall weak coupling constant of less than 0.15, but with a characteristic energy dependence. Derived electronic self-energies compare favorably with previous angle-resolved photoemission spectroscopy results. The prevailing coupling is carried by optical modes of polar character, which is weakly screened by the metallic surface state and can be reduced by doping into bulk bands. We do not find any indication of a strong coupling to the A1g mode or the presence of a Kohn anomaly in the surface phonon spectrum. The weak intrinsic electron-phonon coupling guarantees long-lived quasiparticles at elevated temperatures.

| S-EPMC5430646 | biostudies-literature

Phonon Transport at Crystalline Si/Ge Interfaces: The Role of Interfacial Modes of Vibration.

Project description:We studied the modal contributions to heat conduction at crystalline Si and crystalline Ge interfaces and found that more than 15% of the interface conductance arises from less than 0.1% of the modes in the structure. Using the recently developed interface conductance modal analysis (ICMA) method along with a new complimentary methodology, we mapped the correlations between modes, which revealed that a small group of interfacial modes, which exist between 12-13 THz, exhibit extremely strong correlation with other modes in the system. It is found that these interfacial modes (e.g., modes with large eigen vectors for interfacial atoms) are enabled by the degree of anharmonicity near the interface, which is higher than in the bulk, and therefore allows this small group of modes to couple to all others. The analysis sheds light on the nature of localized vibrations at interfaces and can be enlightening for other investigations of localization.

| S-EPMC4793224 | biostudies-literature

Experimental observation of localized interfacial phonon modes.

Project description:Interfaces impede heat flow in micro/nanostructured systems. Conventional theories for interfacial thermal transport were derived based on bulk phonon properties of the materials making up the interface without explicitly considering the atomistic interfacial details, which are found critical to correctly describing thermal boundary conductance. Recent theoretical studies predicted the existence of localized phonon modes at the interface which can play an important role in understanding interfacial thermal transport. However, experimental validation is still lacking. Through a combination of Raman spectroscopy and high-energy-resolution electron energy-loss spectroscopy in a scanning transmission electron microscope, we report the experimental observation of localized interfacial phonon modes at ~12 THz at a high-quality epitaxial Si-Ge interface. These modes are further confirmed using molecular dynamics simulations with a high-fidelity neural network interatomic potential, which also yield thermal boundary conductance agreeing well with that measured in time-domain thermoreflectance experiments. Simulations find that the interfacial phonon modes have an obvious contribution to the total thermal boundary conductance. Our findings significantly contribute to the understanding of interfacial thermal transport physics and have impact on engineering thermal boundary conductance at interfaces in applications such as electronics thermal management and thermoelectric energy conversion.

| S-EPMC8617064 | biostudies-literature

Coherent phonon dynamics in spatially separated graphene mechanical resonators.

Project description:Vibrational modes in mechanical resonators provide a promising candidate to interface and manipulate classical and quantum information. The observation of coherent dynamics between distant mechanical resonators can be a key step toward scalable phonon-based applications. Here we report tunable coherent phonon dynamics with an architecture comprising three graphene mechanical resonators coupled in series, where all resonators can be manipulated by electrical signals on control gates. We demonstrate coherent Rabi oscillations between spatially separated resonators indirectly coupled via an intermediate resonator serving as a phonon cavity. The Rabi frequency fits well with the microwave burst power on the control gate. We also observe Ramsey interference, where the oscillation frequency corresponds to the indirect coupling strength between these resonators. Such coherent processes indicate that information encoded in vibrational modes can be transferred and stored between spatially separated resonators, which can open the venue of on-demand phonon-based information processing.

| S-EPMC7084087 | biostudies-literature

A self-stabilized coherent phonon source driven by optical forces.

Project description:We report a novel injection scheme that allows for "phonon lasing" in a one-dimensional opto-mechanical photonic crystal, in a sideband unresolved regime and with cooperativity values as low as 10(-2). It extracts energy from a cw infrared laser source and is based on the triggering of a thermo-optical/free-carrier-dispersion self-pulsing limit-cycle, which anharmonically modulates the radiation pressure force. The large amplitude of the coherent mechanical motion acts as a feedback that stabilizes and entrains the self-pulsing oscillations to simple fractions of the mechanical frequency. A manifold of frequency-entrained regions with two different mechanical modes (at 54 and 122?MHz) are observed as a result of the wide tuneability of the natural frequency of the self-pulsing. The system operates at ambient conditions of pressure and temperature in a silicon platform, which enables its exploitation in sensing, intra-chip metrology or time-keeping applications.

| S-EPMC4621534 | biostudies-literature

Coherent optical phonon oscillation and possible electronic softening in WTe2 crystals.

Project description:A rapidly-growing interest in WTe2 has been triggered by the giant magnetoresistance effect discovered in this unique system. While many efforts have been made towards uncovering the electron- and spin-relevant mechanisms, the role of lattice vibration remains poorly understood. Here, we study the coherent vibrational dynamics in WTe2 crystals by using ultrafast pump-probe spectroscopy. The oscillation signal in time domain in WTe2 has been ascribed as due to the coherent dynamics of the lowest energy A1 optical phonons with polarization- and wavelength-dependent measurements. With increasing temperature, the phonon energy decreases due to anharmonic decay of the optical phonons into acoustic phonons. Moreover, a significant drop (15%) of the phonon energy with increasing pump power is observed which is possibly caused by the lattice anharmonicity induced by electronic excitation and phonon-phonon interaction.

| S-EPMC4960623 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data