Publications

2016

Milne, Bruce F; Kjær, Christina; Houmøller, Jørgen; Stockett, Mark H; Toker, Yoni; Rubio, Angel; Nielsen, Steen Brøndsted

On the Exciton Coupling between Two Chlorophyll Pigments in the Absence of a Protein Environment: Intrinsic Effects Revealed by Theory and Experiment Journal Article

Angewandte Chemie, 128 (21), pp. 6356–6359, 2016, ISSN: 1521-3757.

Links | BibTeX | Tags: chlorophyll, photosynthesis

2015

Jornet-Somoza, Joaquim ; Alberdi-Rodriguez, Joseba ; Milne, Bruce F; Andrade, Xavier ; Marques, Miguel A L; Nogueira, Fernando ; Oliveira, Micael J T; Stewart, James J P; Rubio, Angel

Insights into colour-tuning of chlorophyll optical response in green plants Journal Article

Phys. Chem. Chem. Phys., 17 , pp. 26599-26606, 2015.

Abstract | Links | BibTeX | Tags: chlorophyll, light harvesting complex, photosynthesis

Stockett, Mark H; Musbat, Lihi ; Kjær, Christina ; Houmøller, Jørgen ; Toker, Yoni ; Rubio, Angel ; Milne, Bruce F; Brøndsted Nielsen, Steen

The Soret absorption band of isolated chlorophyll a and b tagged with quaternary ammonium ions Journal Article

Phys. Chem. Chem. Phys., 17 , pp. 25793-25798, 2015.

Abstract | Links | BibTeX | Tags: action spectroscopy, chlorophyll, photosynthesis

Milne, Bruce F; Toker, Yoni ; Rubio, Angel ; Brøndsted Nielsen, Steen

Unraveling the Intrinsic Color of Chlorophyll Journal Article

Angewandte Chemie International Edition, 54 (7), pp. 2170–2173, 2015.

Abstract | Links | BibTeX | Tags: action spectroscopy, chlorophyll, photosynthesis

Milne, Bruce F; Norman, Patrick

Resonant-Convergent PCM Response Theory for the Calculation of Second Harmonic Generation in Makaluvamines A–V: Pyrroloiminoquinone Marine Natural Products from Poriferans of Genus Zyzzya Journal Article

The Journal of Physical Chemistry A, 119 (21), pp. 5368-5376, 2015.

Abstract | Links | BibTeX | Tags: marine natural products, nonlinear optics

Martín-Ramos, Pablo ; Silva, Pedro Pereira S; Chamorro-Posada, Pedro ; Ramos Silva, Manuela ; Milne, Bruce F; Nogueira, Fernando ; Martín-Gil, Jesús

Synthesis, structure, theoretical studies and luminescent properties of a ternary erbium(III) complex with acetylacetone and bathophenanthroline ligands Journal Article

Journal of Luminescence, (0), pp. -, 2015, ISSN: 0022-2313.

Abstract | Links | BibTeX | Tags: Erbium, heavy metals, β-diketonate

Stockett, Mark H; Houmøller, Jørgen ; Kjær, Christina ; Milne, Bruce F; Musbat, Lihi ; Rubio, Angel ; Toker, Yoni ; Brøndsted Nielsen, Steen

Action spectroscopy of chlorophyll and other coordination complexes. Journal Article

Journal of Physics: Conference Series, 635 (11), pp. 112015, 2015.

Abstract | Links | BibTeX | Tags: action spectroscopy, chlorophyll, photosynthesis

Santos-Oliveira, Patrícia; Correia, António; Rodrigues, Tiago; Ribeiro-Rodrigues, Teresa Matafome Paulo M; Rodríguez-Manzaneque, Juan Carlos; Seiça, Raquel; Girão, Henrique; Travasso, Rui D M

The Force at the Tip - Modelling Tension and Proliferation in Sprouting Angiogenesis Journal Article

PLoS Comput Biol, 11 (8), pp. e1004436, 2015.

Abstract | Links | BibTeX | Tags:

Rojas, Aimee Torres M; Romero, Alejandro Meza; Pagonabarraga, Ignacio; Travasso, Rui D M; Poiré, Eugenia Corvera

Obstructions in Vascular Networks: Relation Between Network Morphology and Blood Supply Journal Article

PLoS ONE, 10 (6), pp. e0128111, 2015.

Abstract | Links | BibTeX | Tags:

2014

Jensen, Marianne W; Støchkel, Kristian ; Kjær, Christina ; Knudsen, Jeppe L; Maltsev, Oleg V; Hintermann, Lukas ; Naumov, Panče ; Milne, Bruce F; Brøndsted Nielsen, Steen

Photoinduced dissociation mass spectroscopy of firefly oxyluciferin anions Journal Article

International Journal of Mass Spectrometry, 365–366 (0), pp. 3 - 9, 2014, ISSN: 1387-3806, (Special issue: Tilmann mark).

Abstract | Links | BibTeX | Tags: action spectroscopy, bioluminescence, Oxyluciferin

de Lima Ferreira, Marcelle ; Milne, Bruce F; de Souza, Marcus V N; Tiekink, Edward R T; Wardell, James L; Wardell, Solange M S V

Structures of Two Rotamers of the HCl Salt of 4-Methyl-2-[(1E)-[2-(quinolin-4-yl)hydrazin-1-ylidene]methyl]phenol: Different Supramolecular Arrays Journal Article

Journal of Chemical Crystallography, 44 (1), pp. 36-41, 2014, ISSN: 1074-1542.

Abstract | Links | BibTeX | Tags: hydrogen bonding, rotamers

Milne, Bruce F

Enhancement of nonlinear optical properties in late group 15 tetrasubstituted cubanes Journal Article

Dalton Trans., 43 , pp. 6333-6338, 2014.

Abstract | Links | BibTeX | Tags: Antimony, Arsenic, Bismuth, group 15, heavy atom effect, heavy metals, Nitrogen, Phosphorus

Milne, Bruce F

Red-shifting the optical response of firefly oxyluciferin with group 15/16 substitutions Journal Article

Phys. Chem. Chem. Phys., 16 , pp. 24971-24977, 2014.

Abstract | Links | BibTeX | Tags: bioluminescence, group 15, group 16, heavy atom effect, Oxyluciferin

Gandica, Yérali; Schwarz, Tobias; Oliveira, Orlando; Travasso, Rui D M

Hypoxia in Vascular Networks: A Complex System Approach to Unravel the Diabetic Paradox Journal Article

PLoS ONE, 9 (11), pp. e113165, 2014.

Abstract | Links | BibTeX | Tags:

2013

Milne, Bruce F; Nogueira, Fernando ; Cardoso, Claudia

Theoretical study of heavy-atom tuning of nonlinear optical properties in group 15 derivatives of N,N,N-trimethylglycine (betaine) Journal Article

Dalton Trans., 42 , pp. 3695-3703, 2013.

Abstract | Links | BibTeX | Tags: Antimony, Arsenic, Bismuth, group 15, heavy atom effect, Nitrogen, nonlinear optics, Phosphorus

Milne, Bruce F; Norman, Patrick ; Nogueira, Fernando ; Cardoso, Claudia

Marine natural products from the deep Pacific as potential non-linear optical chromophores Journal Article

Phys. Chem. Chem. Phys., 15 , pp. 14814-14822, 2013.

Abstract | Links | BibTeX | Tags: marine natural products, nonlinear optics

Støchkel, Kristian ; Hansen, Christian Nygaard ; Houmøller, Jørgen ; Nielsen, Lisbeth Munksgaard ; Anggara, Kelvin ; Linares, Mathieu ; Norman, Patrick ; Nogueira, Fernando ; Maltsev, Oleg V; Hintermann, Lukas ; Brøndsted Nielsen, Steen ; Naumov, Panče ; Milne, Bruce F

On the Influence of Water on the Electronic Structure of Firefly Oxyluciferin Anions from Absorption Spectroscopy of Bare and Monohydrated Ions in Vacuo Journal Article

J. Am. Chem. Soc., 135 (17), pp. 6485-6493, 2013.

Links | BibTeX | Tags: action spectroscopy, bioluminescence, hydrogen bonding, Oxyluciferin

Flores, Joaquín; Romero, Alejandro Meza; Travasso, Rui D M; Poiré, Eugenia Corvera

Flow and anastomosis in vascular networks Journal Article

Journal of Theoretical Biology, 317 , pp. 257 - 270, 2013, ISSN: 0022-5193.

Abstract | Links | BibTeX | Tags: Viscoelastic flow

2012

Guerra, Dias Soares Quinas M M; Travasso, Rui D M

Novel approach to vascular network modeling in 3D Inproceedings

Bioengineering (ENBENG), 2012 IEEE 2nd Portuguese Meeting in, pp. 1-6, 2012.

Abstract | Links | BibTeX | Tags: activated tip cells, angiogenesis, Biological system modeling, biological tissues, blood vessels, cellular biophysics, chemotactic response, diseases, endothelial cell proliferation, Equations, Evolution (biology), Four equations model, high angiogenic factor consumption, hybrid modeling, hybrid multiscale phase-field model simulation, hypoxic cells, Indexes, Mathematical model, order parameter, phase-field model, physiological models, proangiogenic factor, proliferative vessels, sprout emerging, stroma, three-dimensional, three-dimensional system, vascular network modeling, vascular vessels tree, VEGF

Santos, C; Lavrador, R; Caetano, G; Lori, N F; Travasso, Rui D M

Use of Shannon information to relate function and structure in the brain using diffusion spectrum imaging MRI Inproceedings

Bioengineering (ENBENG), 2012 IEEE 2nd Portuguese Meeting in, pp. 1-4, 2012.

Abstract | Links | BibTeX | Tags: biodiffusion, Biomedical imaging, biomedical MRI, brain, computer simulation, diffusion MRI, diffusion spectrum imaging MRI, DSI, fiber tracking, fiber tracking technology, human brain, Humans, information theory, Magnetic resonance, Magnetic resonance imaging, Mathematical model, medical image processing, neurophysiology, q-ball imaging, QBI, Shannon information, Software, white matter, white matter fiber tracking

Faísca, Patrícia F N; Travasso, Rui D M; Parisi, Andrea; Rey, Antonio

Why Do Protein Folding Rates Correlate with Metrics of Native Topology? Journal Article

PLoS ONE, 7 (4), pp. e35599, 2012.

Abstract | Links | BibTeX | Tags:

Quinas-Guerra, M M; Ribeiro-Rodrigues, T M; Rodríguez-Manzaneque, Juan Carlos; Travasso, Rui D M

Understanding the Dynamics of Tumor Angiogenesis: A Systems Biology Approach Incollection

Azmi, Asfar S (Ed.): Systems Biology in Cancer Research and Drug Discovery, pp. 197-227, Springer Netherlands, 2012, ISBN: 978-94-007-4818-7.

Links | BibTeX | Tags: VEGFR2, VEGFR3 – VEGF receptors; Viscoelastic effects; Wound healing assay

2011

Travasso, Rui D M

The mechanics of blood vessel growth Book Chapter

Simionescu, Dan T; Simionescu, Agneta (Ed.): Vasculogenesis and Angiogenesis – from Embrionic Development to Regenerative Medicine, pp. 187-204, InTech, 2011.

Links | BibTeX | Tags: blood vessels

Støchkel, Kristian ; Milne, Bruce F; Brøndsted Nielsen, Steen

Absorption Spectrum of the Firefly Luciferin Anion Isolated in Vacuo Journal Article

J. Phys. Chem. A, 115 (11), pp. 2155–2159, 2011.

Abstract | Links | BibTeX | Tags: action spectroscopy, bioluminescence, luciferin

Travasso, Rui D M; Poiré, Eugenia Corvera; Castro, Mario; Rodrguez-Manzaneque, Juan Carlos; Hernández-Machado, A

Tumor Angiogenesis and Vascular Patterning: A Mathematical Model Journal Article

PLoS ONE, 6 (5), pp. e19989, 2011.

Abstract | Links | BibTeX | Tags:

Travasso, Rui D M; Castro, Mario; Oliveira, Joana C R E

The phase-field model in tumor growth Journal Article

Philosophical Magazine, 91 (1), pp. 183-206, 2011.

Abstract | Links | BibTeX | Tags:

2010

Olga Kuksenok Rui D. M. Travasso, Pratyush Dayal ; Balazs, Anna C

Modeling the Self-Assembly of Ternary Blends that Encompass Photosensitive Chemical Reactions: Creating Defect-free, Hierarchically Ordered Materials Incollection

Isayev, Avraam I (Ed.): Encyclopaedia of Polymer Blends, 1 , pp. 269, Wiley-VCH, 2010.

Links | BibTeX | Tags: polymer

Travasso, Rui D M

Dinamica do crescimento tumoral: um olhar físico Journal Article

Gazeta de Fisica, 33 (3/4), pp. 18, 2010.

Abstract | Links | BibTeX | Tags: cancer, computer simulation, Mathematical model

Abdel-Mageed, Wael M; Milne, Bruce F; Wagner, Marcell ; Schumacher, Marc ; Sandor, Peter ; Pathom-aree, Wasu ; Goodfellow, Michael ; Bull, Alan T; Horikoshi, Koki ; Ebel, Rainer ; Diederich, Marc ; Fiedler, Hans-Peter ; Jaspars, Marcel

Dermacozines, a new phenazine family from deep-sea dermacocci isolated from a Mariana Trench sediment Journal Article

Org. Biomol. Chem., 8 (10), pp. 2352, 2010, ISSN: 1477-0520.

Links | BibTeX | Tags: marine natural products

Cai, Duanjun ; Marques, Miguel A L; Milne, Bruce F; Nogueira, Fernando

Bioheterojunction Effect on Fluorescence Origin and Efficiency Improvement of Firefly Chromophores Journal Article

Journal of Physical Chemistry Letters, 1 (19), pp. 2781–2787, 2010.

Abstract | Links | BibTeX | Tags: bioluminescence, Oxyluciferin

Cardoso, Claúdia ; Abreu, Paulo E; Milne, Bruce F; Nogueira, Fernando

Computational Study of Molecules with High Intrinsic Hyperpolarizabilities Journal Article

J. Phys. Chem. A, 114 (39), pp. 10676–10683, 2010.

Abstract | Links | BibTeX | Tags: nonlinear optics

Milne, Bruce F; Marques, Miguel A L; Nogueira, Fernando

Fragment molecular orbital investigation of the role of AMP protonation in firefly luciferase pH-sensitivity Journal Article

Phys. Chem. Chem. Phys., 12 (42), pp. 14285, 2010, ISSN: 1463-9076.

Links | BibTeX | Tags: bioluminescence, luciferase, Oxyluciferin

Tadesse, Margey ; Strøm, Morten B; Svenson, Johan ; Jaspars, Marcel ; Milne, Bruce F; Tørfoss, Veronika ; Andersen, Jeanette H; Hansen, Espen ; Stensvåg, Klara ; Haug, Tor

Synoxazolidinones A and B: Novel Bioactive Alkaloids from the Ascidian Synoicum pulmonaria Journal Article

Org. Lett., 12 (21), pp. 4752–4755, 2010.

Abstract | Links | BibTeX | Tags: circular dichroism, marine natural products

Faísca, Patrícia F N; Nunes, Ana; Travasso, Rui D M; Shakhnovich, Eugene I

Non-native interactions play an effective role in protein folding dynamics Journal Article

Protein Science, 19 (11), pp. 2196–2209, 2010, ISSN: 1469-896X.

Abstract | Links | BibTeX | Tags: folding pathways, kinetics, Monte Carlo simulation, native geometry, non-native interactions

Faísca, Patrícia F N; Travasso, Rui D M; Charters, Tiago; Nunes, Ana; Cieplak, Marek

The folding of knotted proteins: insights from lattice simulations Journal Article

Physical Biology, 7 (1), pp. 016009, 2010.

Abstract | Links | BibTeX | Tags:

Travasso, Rui D M; Faísca, Patrícia F N; Rey, Antonio

The protein folding transition state: Insights from kinetics and thermodynamics Journal Article

The Journal of Chemical Physics, 133 (12), pp. 125102, 2010.

Links | BibTeX | Tags:

2009

de Lima, Geraldo M; Milne, Bruce F; Pereira, Robson P; Rocco, Ana Maria ; Skakle, Janet M S; Travis, Anthony J; Wardell, James L; Wardell, Solange M S V

Experimental and ab initio structural study of estertin compounds, X3SnCH2CH2CO2Me: Crystal structures of Cl3SnCH2CH2CO2Me at 120 K and Br3SnCH2CH2CO2Me at 120 and 291 K Journal Article

J. Mol. Struct., 921 (1-3), pp. 244–250, 2009.

Abstract | Links | BibTeX | Tags: Tin

2008

Krupp, Eva ; Milne, Bruce F; Mestrot, Adrien ; Meharg, Andrew ; Feldmann, Jørg

Investigation into mercury bound to biothiols: structural identification using ESI-ion-trap MS and introduction of a method for their HPLC separation with simultaneous detection by ICP-MS and ESI-MS Journal Article

Anal. Bioanal. Chem., 390 (7), pp. 1753–1764, 2008.

Abstract | Links | BibTeX | Tags: heavy metals, Mercury

Latifi, Reza ; Bagherzadeh, Mojtaba ; Milne, Bruce F; Jaspars, Marcel ; de Visser, Sam P

Density functional theory studies of oxygen and carbonate binding to a dicopper patellamide complex Journal Article

J. Inorg. Biochem., 102 (12), pp. 2171–2178, 2008.

Abstract | Links | BibTeX | Tags: Carbonate, Copper, Oxygen, Tyrosinase

Wright, Stephen H; Raab, Andrea ; Tabudravu, Jioji N; Feldmann, Jørg ; Long, Paul F; Battershill, Christopher N; Dunlap, Walter C; Milne, Bruce F; Jaspars, Marcel

Marine Metabolites and Metal Ion Chelation: Intact Recovery and Identification of an Iron(II) Complex in the Extract of the Ascidian Eudistoma gilboviride Journal Article

Angew. Chem. Int. Ed., 47 (42), pp. 8090–8092, 2008.

Abstract | Links | BibTeX | Tags: circular dichroism, marine natural products

Oliveira, J C R E; Braga, M H; Travasso, Rui D M

Simulation of the spinodal phase separation dynamics of the Bi-€“Zn system Journal Article

Journal of Non-Crystalline Solids, 354 (47-€“51), pp. 5340 - 5342, 2008, ISSN: 0022-3093, (Non-Crystalline Solids 9 Proceedings of the 9th International Workshop on Non-Crystalline Solids9th International Workshop on Non-Crystalline Solids).

Abstract | Links | BibTeX | Tags: Surfaces and interfaces

Faísca, Patrícia F N; Travasso, Rui D M; Ball, R C; Shakhnovich, E I

Identifying critical residues in protein folding: Insights from ϕ-value and Pfold analysis Journal Article

The Journal of Chemical Physics, 129 (9), pp. 095108, 2008.

Links | BibTeX | Tags:

2007

Regmi, Rajendra ; Milne, Bruce F; Feldmann, Jørg

Hydride generation activity of arsenosugars and thioarsenicals Journal Article

Anal. Bioanal. Chem., 388 (4), pp. 775–782, 2007.

Abstract | Links | BibTeX | Tags: Arsenic, marine natural products

Travasso, Rui D M; da Gama, Margarida Telo M; Faí­sca, Patr'­cia F N

Pathways to folding, nucleation events, and native geometry Journal Article

The Journal of Chemical Physics, 127 (14), pp. -, 2007.

Links | BibTeX | Tags:

Travasso, Rui D M; Faí­sca, Patrí­cia F N; da Gama, Margarida Telo M

Nucleation phenomena in protein folding: the modulating role of protein sequence Journal Article

Journal of Physics: Condensed Matter, 19 (28), pp. 285212, 2007.

Abstract | Links | BibTeX | Tags: