Biophysics - Organics

Articles ...

Influence of transition mutations and disorder on charge localization and transfer along B-DNA sequences

P. Banev, A. Falliera, and C. Simserides*

Physica Scripta 100 (2025) 075992 (20 pages) doi: 10.1088/1402-4896/ade63e 

QuantumDNA: A Python Package for Analyzing Quantum Charge Dynamics in DNA and Exploring Its Biological Relevance

D. Herb, M. Trenti, M. Mantela, C. Simserides, J. Ankerhold, M. Rossini

Computer Physics Communications 313 (2025) 109626 (16 pages) doi: 10.1016/j.cpc.2025.109626

Four-channel model: An assessment of charge transfer via the backbone in B-DNA

A. Kordas, A. Morphis, and C. Simserides*

Physical Review E 111 (2025) 024414 (11 pages) doi: 10.1103/PhysRevE.111.024414

Plus, Supplemental Material (11 pages)

Electronic structure, absorption spectra and oxidation dynamics in polyynes and dicyanopolyynes

L. Chalkopiadis, K. Lambropoulos and C. Simserides*

Physical Chemistry Chemical Physics 26 (2024) 22149 - 22163 doi: 10.1039/D4CP02719A

We also published a Correction, 

Physical Chemistry Chemical Physics 27 (2025) 6372-6372 doi: 10.1039/d5cp90049b

Charge transport in a double-stranded DNA: Effects of helical symmetry and long-range hopping

S. Kundu and C. Simserides

Physical Review E 109 (2024) 014401 doi: 10.1103/PhysRevE.109.014401

Electronic Structure and Hole Transfer of All B-DNA Dimers and Homopolymers, via the Fishbone-Wire Model

C. Simserides*, A. Orfanaki, N. Margariti, K. Lambropoulos

Materials 16 (2023) 3200 (25 pages) doi: 10.3390/ma16083200 

Charge transport properties of ideal and natural DNA segments, as mutation detectors 

M. Mantela, K. Lambropoulos, C. Simserides* 

Physical Chemistry Chemical Physics 25 (2023) 7750-7762 doi: 10.1039/D3CP00268C

Energy Transport along α-Helix Protein Chains: 

External Drives and Multifractal Analysis

N. Sefidkar, S. Fathizadeh*, F. Nemati, C. Simserides

Materials 15 (2022) 2779 (13 pages) doi: 10.3390/ma15082779

Cyclo[18]carbon including Zero-Point Motion: 

Ground State, First Singlet and Triplet Excitations, and Hole Transfer

K. Lambropoulos*, A. M. Alvertis, A. Morphis, C. Simserides

Physical Chemistry Chemical Physics 24 (2022) 7779-7787 doi: 10.1039/D2CP00343K

LCAO electronic structure of nucleic acid bases and other heterocycles and transfer integrals in B-DNA, including structural variability

M. Mantela, C. Simserides*, R. Di Felice*

Materials 14 (2021) 4930 (20 pages) doi: 10.3390/ma14174930

Effects of structural dynamics on charge carrier transfer in B-DNA: a combined MD and RT-TDDFT study

M. Mantela, A. Morphis, K. Lambropoulos, C. Simserides*, R. Di Felice*

The Journal of Physical Chemistry B 125 (2021) 3986-4003

doi: 10.1021/acs.jpcb.0c11489

Hole transfer in open carbynes

C. Simserides*, A. Morphis, K. Lambropoulos

Materials 13 (2020) 3979 (24 pages)

doi: 10.3390/ma13183979

Hole Transfer in Cumulenic and Polyynic Carbynes

C. Simserides*, A. Morphis, K. Lambropoulos

The Journal of Physical Chemistry 124 (2020) 12834−12849

doi: 10.1021/acs.jpcc.0c03763

Tight-Binding modeling of nucleic acid sequences: 

interplay between various types of order or disorder and charge transport

K. Lambropoulos* and C. Simserides*

Symmetry 11 (2019) 968 (26 pages)

doi: 10.3390/sym11080968

Invited Review to the special issue of Symmetry, 

Symmetry and Asymmetry in Quasicrystals or Amorphous Materials, 

with guest Editor Enrique Macia.

Quasi-periodic and fractal polymers: Energy structure and carrier transfer

M. Mantela, K. Lambropoulos, M. Theodorakou, C. Simserides*

Materials 12 (2019), 2177 (30 pages) 

doi: 10.3390/ma12132177

Periodic, quasiperiodic, fractal, Kolakoski, and random binary polymers: 

Energy structure and carrier transport

K. Lambropoulos and C. Simserides* 

Physical Review E 99 (2019) 032415 (17 pages)

doi: 10.1103/PhysRevE.99.032415

Academy of Athens, Lycurgus Award, 2022, for original research in Theoretical Physics. 

Periodic polymers with increasing repetition unit: 

Energy structure and carrier transfer 

K. Lambropoulos, C. Vantaraki, P. Bilia, M. Mantela, C. Simserides*

Physical Review E 98 (2018) 032412 (14 pages + 23 pages Supplemental Material) 

doi: 10.1103/PhysRevE.98.032412

Spectral and transmission properties of periodic 1D Tight-Binding lattices with 

a generic unit cell: an analysis within the transfer matrix approach

K. Lambropoulos* and C. Simserides*

Journal of Physics Communications 2 (2018) 035013 (19 pages)

doi: 10.1088/2399-6528/aab065

Electronic structure and charge transport properties of atomic carbon wires

K. Lambropoulos and C. Simserides*

Physical Chemistry Chemical Physics 19 (2017) 26890 - 26897

doi: 10.1039/c7cp05134d

MOVIE: hole oscillations within the AT dimer produced by RT-TDDFT

MOVIE: hole oscillations within the GA dimer produced by RT-TDDFT 

RT-TDDFT study of hole oscillations in B-DNA monomers and dimers

M. Tassi*, A. Morphis, K. Lambropoulos, C. Simserides

Cogent Physics 4 (2017) 1361077 (12 pages)

doi: 10.1080/23311940.2017.1361077 

Electronic structure and carrier transfer in B-DNA monomer polymers and dimer polymers: Stationary and time-dependent aspects of wire model vs. extended ladder model

K. Lambropoulos, M. Chatzieleftheriou, A. Morphis, K. Kaklamanis, R. Lopp, M. Theodorakou, M. Tassi, C. Simserides*

Physical Review E 94 (2016) 062403 (22 pages)

doi: 10.1103/PhysRevE.94.062403

Wire and extended ladder model predict THz oscillations in DNA monomers, dimers and trimers

K. Lambropoulos, K. Kaklamanis, A. Morphis, M. Tassi, R. Lopp, G. Georgiadis, M. Theodorakou, M. Chatzieleftheriou, C. Simserides*

Journal of Physics: Condensed Matter 28 (2016) 495101 (19 pages)

doi: 10.1088/0953-8984/28/49/495101

Lowest ionization and excitation energies of biologically important heterocyclic planar molecules

M. Mantela, A. Morphis, M. Tassi, C. Simserides*

Molecular Physics 114 (2016) 709-718

doi: 10.1080/00268976.2015.1113313 

Unbiased charge oscillations in DNA monomer polymers and dimer polymers

K. Lambropoulos, M. Chatzieleftheriou, A. Morphis, K. Kaklamanis, M. Theodorakou, C. Simserides*

Physical Review E 92 (2015) 032725 (16 pages)

doi: 10.1103/PhysRevE.92.032725

THz and above THz electron or hole oscillations in DNA dimers and trimers

K. Lambropoulos, K. Kaklamanis, G. Georgiadis, C. Simserides*

Annalen der Physik (Berlin) 526 (2014) 249–258

doi: 10.1002/andp.20140006A7

A systematic study of electron or hole transfer along DNA dimers, trimers and polymers

C. Simserides*

Chemical Physics 440 (2014) 31-41

doi: 10.1016/j.chemphys.2014.05.024

Density of states and extent of wave function: two crucial factors for small polaron hopping conductivity in 1D

M. Dimakogianni, C. Simserides*, G. P. Triberis

Philosophical Magazine, 93 (2013) 2729-2748

doi: 10.1080/14786435.2013.785639

Academy of Athens Georgios Th. Foteinos Award, 2014, for original research in Experimental or Theoretical Physics.

Electronic parameters for charge transfer along DNA

L. G. D. Hawke, G. Kalosakas*, C. Simserides

European Physical Jouranl E 032 (2010) 291–305

doi: 10.1140/epje/i2010-10650-y

Empirical LCAO parameters for p molecular orbitals in planar organic molecules

L. G. D. Hawke, G. Kalosakas*, C. Simserides

Molecular Physics 107 (2009) 1755–1771

doi: 10.1080/00268970903049089

The π-π* molecular structure of flavin of FADH- enzymatic cofactor using the LCAO method

L. G. D. Hawke, C. Simserides*, G. Kalosakas

Materials Science and Engineering B 165 (2009) 266–269

doi: 10.1016/j.mseb.2009.02.012

Effects of the task of categorizing FM direction on auditory evoked magnetic fields in the human auditory cortex

R. Koenig, C. Sielużycki*, C. Simserides, P. Heil, H. Scheich

Brain Research 1220 (2008) 102-117

doi: 10.1016/j.brainres.2008.02.086

A small polaron hopping model for multiphonon-assisted transport along DNA molecules, in the presence of disorder

G. Triberis, C. Simserides*, V. Karavolas

Physica E: Low-dimensional Systems and Nanostructures 32 (2006) 592–595

doi: 10.1016/j.physe.2005.12.111

Small polaron hopping transport along DNA molecules

G. P. Triberis*, C. Simserides, V. C. Karavolas

J. Phys.: Condens. Matter 17 (2005) 2681-2690

doi: 10.1088/0953-8984/17/17/016

Proceedings ...

Proceedings of ANBRE21 (Arch Eng, Nano, Bio, Robotics & Energy). 

The 2021 International Conference on Advances in Biomaterials and Biomechanics in Bioengineering (ICBME21), 

Seoul National University, Korea, August 23-26, 2021.

C. Simserides*, A. Morphis, K. Lambropoulos. 

Hole Transfer in Open Cumulenic and Polyynic Carbyne Chains. 

Frequency Content of Carrier Oscillations along B-DNA Aperiodic and Periodic Polymers

M. Mantela, K. Lambropoulos, C. Vantaraki, P. Bilia, A. Morphis, C. Simserides*

PIERS (PhotonIcs and Electromagnetics Research Symposium, aka 

Progress In Electromagnetics Research Symposium), 17-20 June 2019, Rome, Italy.

pp. 831-838, doi: 10.1109/PIERS-Spring46901.2019.9017899

URL: http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=9017899&isnumber=9017213

Honorable Mention Student Paper (Antennas & Microwave Technologies) for M. Mantela

Frequency Content of Carrier Oscillations along B-DNA Polymers

K. Lambropoulos, M. Mantela, C. Simserides*

PIERS (Progress in Electromagnetics Research Symposium) Proceedings, 

19- 22 November 2017, Singapore. 

Volume 2018-November, 2018, Pages 186-193. 

doi: 10.1109/PIERS-FALL.2017.8293134

THz oscillations in DNA monomers, dimers and trimers

K. Lambropoulos, K. Kaklamanis, G. Georgiadis, M. Theodorakou, M. Chatzieleftheriou, M. Tassi, A. Morphis, C. Simserides*

PIERS (Progress in Electromagnetics Research Symposium) Proceedings, 6-9 July 2015, Prague, pp 879-833

Best Student Paper Award (Optics and Photonics) for K. Lambropoulos

The effect of a categorical discrimination task on the auditory M100 peak latency

R. König*, C. Sielużycki, C. Simserides, H. Scheich, 

International Congress Series 1300 (2007) 45-48 doi: 10.1016/j.ics.2007.01.062 

Proceedings of BIOMAG 2006 (15th International Conference on Biomagnetism)

High temperature electrical conductivity due to small polaron hopping motion in DNA molecules

G. P. Triberis*, V. C. Karavolas, C. Simserides

Journal of Physics: Conference Series 10 (2005) 210–213 (with referee)

doi: 10.1088/1742-6596/10/1/052 

Proceedings of the 2nd Conf. on Microelectronics, Microsystems and Nanotechnology 2004

Do stimuli or tasks determine lateralized auditory cortex responses? An MEG study

C. Sielużycki, R. König, C. Simserides, H. Scheich

International Journal of Bioelectromagnetism, IJBEM 7 (2005) 185-188

[Proceedings of the Joint Meeting of 5th International Conference on Bioelectromagnetism and 5th International Symposium on Noninvasive Functional Source Imaging within the Human Brain and Heart (BEM & NFSI), University of Minnesota, Twin Cities campus in Minneapolis, Minnesota, USA, 12-15/5/2005]. 

An MEG study of directional categorization of frequency-modulated tones

C. Simserides, R. König, and H. Scheich

Proceedings of the 14th International Conference on Biomagnetism (BIOMAG 2004), 

E. Halgren, S. Ahlfors, M. Hämäläinen, and D. Cohen (eds.), pp. 543-544. Boston: Biomag 2004 Ltd.

Task-dependent activation of the auditory cortex by frequency-modulated tones: an MEG study

C. Simserides*, R. König, and H. Scheich

Biomedizinische Technik 48 (2004) 205-207 (with referee)

Proceedings of NFSI-2003 (4th International Symposium on Nonivasive Functional Source Imaging)

Auditory Cortex Response to Frequency-Modulated Tones Investigated with MEG

R. König, C. Simserides, and H. Scheich

Proceedings of the International Conference on Auditory Cortex, Shaker Verlag, Aachen, Germany (2003) p.30 (13-17 September 2003, Magdeburg, Germany)

Tight-binding parameters for charge transport in DNA, 

L. G. D. Hawke, G. Kalosakas, C. Simserides 

5th Conference of the Hellenic Society for Computational Biology and Bioinformatics, 17-19 October 2010, Alexandroupolis, Greece

A few related older presentations ...

Progress in Electromagnetics Research Symposium (PIERS 2017), 19- 22 November 2017, Nanyang Technological University, Singapore. 

Two TB Approaches (a Wire Model and an Extended Ladder Model) as Well as RT-TDDFT, Predict THz Oscillations in DNA Monomers, Dimers and Trimers. 

and 

Frequency Content of Carrier Oscillations along B-DNA Polymers. 

Mediterranean Institute of Fundamental Physics (MIFP), March Meeting 2017, 8-11 March 2017, Castelli Romani, Rome, Hotel Helio Cabala.

Charge transfer - THz oscillations in DNA segments

EMN Open Access Week (2014) Chengdu

Systematic study of carrier transfer in DNA polymers

NN14 (2014) Thessaloniki

THz and above THz electron or hole oscillations in DNA dimers and trimers

MIFP March Meeting (2011) Rome

Tight binding parameters for charge transport along DNA

MSS-12 (2005) Albuquerque

A small polaron hopping model for the multiphonon-assisted transport along DNA molecules, in the presence of disorder

SOUND PROPERTIES: An encyclopaedic narration, (2002-2004) Magdeburg

part1

part2

part3

part4