Protonic transport through solitons in hydrogen-bonded systems

Kavitha, L.; Jayanthi, S.; Muniyappan, A.; Gopi, D.

doi:10.1088/0031-8949/84/03/035803

Cited by 30 publications

(13 citation statements)

References 40 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Proton motion is known to be responsible for the energy and charge transfer in many HB chains [44]. The conduction via proton migration along the chain in HB systems appears as:…”

Section: Mathematical Background Of Proton Dynamicsmentioning

confidence: 99%

Nano breathers and molecular dynamics simulations in hydrogen-bonded chains

Kavitha¹,

Muniyappan²,

Prabhu³

et al. 2012

J Biol Phys

View full text Add to dashboard Cite

Non-linear localization phenomena in biological lattices have attracted a steadily growing interest and their existence has been predicted in a wide range of physical settings. We investigate the non-linear proton dynamics of a hydrogen-bonded chain in a semiclassical limit using the coherent state method combined with a Holstein-Primakoff bosonic representation. We demonstrate that even a weak inherent discreteness in the hydrogenbonded (HB) chain may drastically modify the dynamics of the non-linear system, leading to instabilities that have no analog in the continuum limit. We suggest a possible localization mechanism of polarization oscillations of protons in a hydrogen-bonded chain through modulational instability analysis. This mechanism arises due to the neighboring protonproton interaction and coherent tunneling of protons along hydrogen bonds and/or around heavy atoms. We present a detailed analysis of modulational instability, and highlight the role of the interaction strength of neighboring protons in the process of bioenergy localization. We perform molecular dynamics simulations and demonstrate the existence of nanoscale discrete breather (DB) modes in the hydrogen-bonded chain. These highly

show abstract

“…Proton motion is known to be responsible for the energy and charge transfer in many HB chains [44]. The conduction via proton migration along the chain in HB systems appears as:…”

Section: Mathematical Background Of Proton Dynamicsmentioning

confidence: 99%

Nano breathers and molecular dynamics simulations in hydrogen-bonded chains

Kavitha¹,

Muniyappan²,

Prabhu³

et al. 2012

J Biol Phys

View full text Add to dashboard Cite

show abstract

“…Kavitha et al also reported the solitonic dynamics of the chain polarization in HB systems, when tunnel processes prevail over the thermal activation and analyzed the tunneling between two opposite directions governed by a bistable potential system at low temperature [2,5]. They suggested a possible coherent tunneling mechanism of spontaneous polarization oscillations of HB chain.…”

Section: B(x T)mentioning

confidence: 99%

“…A special property of PGs is their ability to form HBs [2] with each other, and with water and other molecules in the environment. The study of HB chains [3][4][5] can lead to insight regarding how local interactions can dictate global features of PCs and proteins. Basically, PCs of protein structures [6] are the major workers within the cells, and carry out the functions described by the genetic codes: providing structural support, transmitting signals, catalyzing reactions, and transporting molecules.…”

Section: Introductionmentioning

confidence: 99%

Energy transport mechanism in the form of proton soliton in a one-dimensional hydrogen-bonded polypeptide chain

et al. 2015

View full text Add to dashboard Cite

The dynamics of protons in a one-dimensional hydrogen-bonded (HB) polypeptide chain (PC) is investigated theoretically. A new Hamiltonian is formulated with the inclusion of higher-order molecular interactions between peptide groups (PGs). The wave function of the excitation state of a single particle is replaced by a new wave function of a two-quanta quasi-coherent state. The dynamics is governed by a higher-order nonlinear Schrödinger equation and the energy transport is performed by the proton soliton. A nonlinear multiple-scale perturbation analysis has been performed and the evolution of soliton parameters such as velocity and amplitude is explored numerically. The proton soliton is thermally stable and very robust against these perturbations. The energy transport by the proton soliton is more appropriate to understand the mechanism of energy transfer in biological processes such as muscle contraction, DNA replication, and neuro-electric pulse transfer on biomembranes.

show abstract

“…Most recently Soliman (Soliman, 2006) and El-Wakil (El-Wakil et al, 2005) modified the extended tanh-function method and obtained some new exact traveling wave solutions. We employ the modified extended tanh-function (METF) method (Soliman, 2006;El-Wakil et al, 2005;Kavitha et al, 2011bKavitha et al, , 2012 to solve the Eq. 12which governs the dynamics of director oscillations with elastic deformations such as splay, twist and bend.…”

Section: Shape Changing Solitary Oscillationsmentioning

confidence: 99%

Shape changing nonlocal molecular deformations in a nematic liquid crystal system

Kavitha

Venkatesh

Gopi

2015

Journal of the Association of Arab Universities for Basic and A

View full text Add to dashboard Cite

The nature of nonlinear molecular deformations in a homeotropically aligned nematic liquid crystal (NLC) is presented. We start from the basic dynamical equation for the director axis of a NLC with elastic deformation and mapped onto a integro-differential perturbed Nonlinear Schro¨dinger equation which includes the nonlocal term. By invoking the modified extended tangent hyperbolic function method aided with symbolic computation, we obtain a series of solitary wave solutions. Under the influence of the nonlocality induced by the reorientation nonlinearity due to fluctuations in the molecular orientation, the solitary wave exhibits shape changing property for different choices of parameters. This intriguing property as a result of the relation between the coherence of the solitary deformation and the nonlocality reveals a strong need for a deeper understanding in the theory of self-localization in NLC systems.

show abstract

Protonic transport through solitons in hydrogen-bonded systems

Cited by 30 publications

References 40 publications

Nano breathers and molecular dynamics simulations in hydrogen-bonded chains

Nano breathers and molecular dynamics simulations in hydrogen-bonded chains

Energy transport mechanism in the form of proton soliton in a one-dimensional hydrogen-bonded polypeptide chain

Shape changing nonlocal molecular deformations in a nematic liquid crystal system

Contact Info

Product

Resources

About